Powers Wiki - User contributions [en]

One way ANOVA in R

2015-11-11T23:41:16Z

Teklab:

The one way analysis of variance is used to test if three or more means are equal. One way ANOVA is an extension of two independent samples t-test.

===using R===
*Open the R console
*Change the working directory to the directory where your file is"

setwd('C:/Users/yourfolder')

*Read the file: E.g the file used here is smaple.csv. The file has three groups with the following format

{| class="wikitable"
|-
! Header 1
! Header 2
! Header 3
|-
| a
| b
| c
|-
| d
| e
| f
|}
* Read the file and name it (e.g metab)
metab <- read.csv ("sample.csv, header= T)
* confirm the file is imported. When you call for metab and press enter you should see the table
*make box plot
boxplot(metab)
*Then use the following command to conduct one way anova and Tukey's test
smetab <- stack(metab) 
names(smetab) <- c("length", "group") 
smetab 
av1<-aov(length ~ group, data=smetab) 
summary(av1) 
tk<- TukeyHSD(av1) 
tk 
[[Category:Protocols]]
[[Category:Metabolomics]]

One way ANOVA in R

2015-11-11T23:40:53Z

Teklab:

One way ANOVA in R

2015-11-11T23:40:12Z

Teklab:

MetPa for metabolomics

2015-11-11T19:20:44Z

Teklab:

*To use metpa for metabolomics pathway analysis go to http://metpa.metabolomics.ca/MetPA/faces/Home.jsp
*enter the list of metabolites using Keeg or HMDB id (using metabolite names is sometime confusing)
*select the pathway library according to the organism of interest
*select the overepresentation and topology analysis
*submit the data
[[Category:Protocols]]
[[Category:Metabolomics]]

MetPa for metabolomics

2015-11-11T19:18:56Z

Teklab:

MetPa for metabolomics

2015-11-11T19:17:46Z

Teklab: Created page with "*To use metapa for metabolomics pathway analysis go to http://metpa.metabolomics.ca/MetPA/faces/Home.jsp *enter the list of metabolites using Keeg or HMDB id (using metabolite..."

*To use metapa for metabolomics pathway analysis go to http://metpa.metabolomics.ca/MetPA/faces/Home.jsp
*enter the list of metabolites using Keeg or HMDB id (using metabolite names is sometime confusing)
*select the pathway library accoridn to the organism of interest
*select the overrepresentation and topology analysis
*submit the data

One way ANOVA in R

2015-11-11T18:58:20Z

Teklab:

One way ANOVA in R

2015-11-11T18:56:57Z

Teklab:

One way ANOVA in R

2015-11-11T18:56:07Z

Teklab: Created page with "The one way analysis of variance is used to test if three or more means are equal. One way ANOVA is an extension of two independent samples t-test. ===using R=== *Open the R ..."

The one way analysis of variance is used to test if three or more means are equal. One way ANOVA is an extension of two independent samples t-test.

===using R===
*Open the R console
*Change the working directory to the directory where your file presents using the following command"

setwd('C:/Users/yourfolder')

*Read the file: E.g the file used here is smaple.csv. The file has three groups with the following format

{| class="wikitable"
|-
! Header 1
! Header 2
! Header 3
|-
| a
| b
| c
|-
| d
| e
| f
|}
* Read the file and name it (e.g metab)
metab <- read.csv ("sample.csv, header= T)
* confirm the file is imported. When you call for metab and press enter you should see the table
*make box plot
boxplot(metab)
*Then use the following command to conduct one way anova and Tukey's test
smetab <- stack(metab) 
names(smetab) <- c("length", "group") 
smetab 
av1<-aov(length ~ group, data=smetab) 
summary(av1) 
tk<- TukeyHSD(av1) 
tk

Main Page

2014-06-17T22:00:30Z

Teklab: /* Wiki Categories */

'''Welcome to the BioNMR Wiki Page.'''

This wiki exists to provide better access to lab protocols for the Powers lab. It is not a replacement for lab notebooks. Feel free to begin documenting new lab protocols or procedures here, or even moving old protocols onto this wiki.

== Getting started ==
For those who need a quick and dirty introduction to MediaWiki formatting, try this reference card:
* [http://bionmr.unl.edu/w/MediaWikiRefCard.pdf MediaWiki Reference Card]

Other general MediaWiki information pages:
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]

=== Wiki Categories ===

[[Special:Categories|View All Categories]]

Commonly used Categories:

* [[:Category:Protocols|Protocols]]
* [[:Category:Bioscreen|Bioscreen]]
* [[:Category:FAST-NMR|FAST-NMR]]
* [[:Category:Molecular Docking|Molecular Docking]]
* [[:Category:Metabolomics|Metabolomics]]
* [[:Category:Maxey Demos|Maxey Demos]]
* [[:Category:Protein expression|Protein expression]]
* [[:Category:SMACMS|SMACMS]]
* [[:Category:Lab Safty | Lab Safty]]

Agarose Gel

2014-02-17T22:10:30Z

Teklab: /* Preparing 1% Agarose Gel */

[[Category:Protocols]]
[[Category:Protein expression]]

==Preparing 1% Agarose Gel==

#Measure 0.6 g of agarose
# Pour the agarose powder into microwavable flask with 60 mL of 1XTAE buffer
#Microwave for 1- 3 min (until the agarose is completely dissolved)
#Cool down the agarose and add ethidium bromide to a final concentration of approximately 0.2 to 0.5 ug/mL
# Pour the agarose into a gel try with the well comb in place
#Let sit at room temperature for about half an hour

'''N.B''' Ethidium bromide is a known mutagen.

==Running Agarose Gel==

# add running buffer to the gel apparatus
# carefully load samples in to the well
# load marker
#

Agarose Gel

2014-02-17T19:58:59Z

Teklab:

Agarose Gel

2014-02-17T19:58:04Z

Teklab: Created page with "==Preparing 1% Agarose Gel== #Measure 0.6 g of agarose # Pour the agarose powder into microwavable flask with 60 mL of 1XTAE buffer #Microwave for 1- 3 min (until the agarose..."

==Preparing 1% Agarose Gel==

#Measure 0.6 g of agarose
# Pour the agarose powder into microwavable flask with 60 mL of 1XTAE buffer
#Microwave for 1- 3 min (until the agarose is completely dissolved)
#Cool down the agarose and add ethidium bromide to a final concentration of approximately 0.2 to 0.5 ug/mL
# Pour the agarose into a gel try with the well comb in place
#Let sit at room temperature for about half an hour

'''N.B''' Ethidium bromide is a known mutagen.

Ligation

2014-02-17T19:50:01Z

Teklab: /* Ligation Protocol with T4 DNA Ligase */

[[Category:Protocols]]
[[Category:Protein expression]]

==Ligation Protocol with T4 DNA Ligase==

#Set up the following reaction in a microcentrifuge tube on ice.
## 2uL of 10X T4 DNA ligase Buffer
## 50 ng 50 ng (0.025 pmol) vector DNA (3 kb)
## 50 ng (0.076 pmol) insert DNA (1 kb)
## 1 uL of T4 DNA Ligase
## add nuclease-free water to make the total volume 20 uL
#Gently mix the reaction by pipetting up and down and microfuge briefly.
#For cohesive (sticky) ends, incubate at 16°C overnight or room temperature for 10 minutes.
#For blunt ends or single base overhangs, incubate at 16°C overnight or room temperature for 2 hours(alternatively, high concentration T4 DNA Ligase can be used in a 10 minute ligation).

'''N.B''' (T4 DNA Ligase should be added last. Note that the table shows a ligation using a molar ratio of 1:3 vector to insert.)

==troubleshooting==

#to avoid frequent thawing and freezing of the ligase buffer, prepare working stock of ligation buffer

Ligation

2014-02-17T19:44:42Z

Teklab: Created page with "==Ligation Protocol with T4 DNA Ligase== #Set up the following reaction in a microcentrifuge tube on ice. ## 2uL of 10X T4 DNA ligase Buffer ## 50 ng 50 ng (0.025 pmol) vecto..."

==Ligation Protocol with T4 DNA Ligase==

#Set up the following reaction in a microcentrifuge tube on ice.
## 2uL of 10X T4 DNA ligase Buffer
## 50 ng 50 ng (0.025 pmol) vector DNA (3 kb)
## 50 ng (0.076 pmol) insert DNA (1 kb)
## 1 uL of T4 DNA Ligase
## add nuclease-free water to make the total volume 20 uL
#Gently mix the reaction by pipetting up and down and microfuge briefly.
#For cohesive (sticky) ends, incubate at 16°C overnight or room temperature for 10 minutes.
#For blunt ends or single base overhangs, incubate at 16°C overnight or room temperature for 2 hours(alternatively, high concentration T4 DNA Ligase can be used in a 10 minute ligation).

'''N.B''' (T4 DNA Ligase should be added last. Note that the table shows a ligation using a molar ratio of 1:3 vector to insert.)

==troubleshooting==

#to avoid frequent thawing and freezing of the ligase buffer, prepare working stock of ligation buffer

Running SDS-PAGE

2014-02-17T15:31:16Z

Teklab: /* Running SDS-PAGE */

[[Category:Protocols]]
[[Category:Protein expression]]

==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the combs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

===Troubleshoot===
#The power drops to zero
* really old buffer
* the space in between the gels is not filled with buffer to the top

Running SDS-PAGE

2014-02-17T15:04:39Z

Teklab:

Running SDS-PAGE

2014-02-17T14:57:16Z

Teklab: Created page with "Category:Protocols Category:Protein expression ==Running SDS-PAGE== #Make ready the samples to run #Make ready the sample running buffer #Make ready the gel #Have th..."

[[Category:Protocols]]
[[Category:Protein expression]]

==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the cumbs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

Category:Protein expression

2014-02-17T14:48:47Z

Teklab: Blanked the page

Category:Protein expression

2014-02-17T14:45:10Z

Teklab:

[[Category:Protocols]]
[[Category:Protein expression]]

==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the cumbs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

Category:Protein expression

2014-02-17T14:44:17Z

Teklab:

==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the cumbs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

Category:Protein expression

2014-02-17T14:42:00Z

Teklab: Blanked the page

Category:Protein expression

2014-02-17T14:41:39Z

Teklab: /* Running SDS-PAGE */

[[Category:Protocols]]
[[Category:Protein expression]]

Category:Protein expression

2014-02-17T14:40:59Z

Teklab:

[[Category:Protocols]]
[[Category:Protein expression]]

==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the cumbs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

Category:Protein expression

2014-02-17T14:36:08Z

Teklab: Blanked the page

Category:Protein expression

2014-02-17T14:35:09Z

Teklab:

[http://www.example.com Running SDS-PAGE]

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the cumbs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

Category:Protein expression

2014-02-17T14:26:15Z

Teklab: Blanked the page

Category:Protein expression

2014-02-17T14:25:00Z

Teklab:

==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#Fill the space between the gels with running buffer
#Take off the combs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#Fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
##'''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source

#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
##The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current and the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

Making Heatmaps

2012-12-04T05:20:40Z

Teklab:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

heatmapname <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(heatmapname) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

heatmapname <- heatmapname [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

heatmapname_matrix <- data.matrix (heatmapname)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (heatmapname_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

'''Note: To rescale the color key, add break function to the heatmap.2. '''

'''breaks=c(seq(-1,0.8,length=10),seq(0.8,1.2,length=10),seq(1.2,3,length=10),'''

This will define the color range:

"red=[-1,0.8]

black=[0.8,1.2]

green=[1.2,3]"

[[Category:Protocols]]
[[Category:Metabolomics]]

==Run from text file==
'''Note: It is also possible to write all the steps in txt file as a single script.'''
===Open the script ===
* In the file menu click open script
** Choose the proper directory and script file name
** The script file will be opened in the R Editor window
** If necessary changes can be made on the R Editor window

===Run the script ===
* Click Run all or Run line or selection form the Edit menu

Making Heatmaps

2012-12-04T05:20:09Z

Teklab:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

heatmapname <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(heatmapname) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

heatmapname <- heatmapname [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

heatmapname_matrix <- data.matrix (heatmapname)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (heatmapname_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

'''Note: To rescale the color key, add break function to the heatmap.2. '''

'''breaks=c(seq(-1,0.8,length=10),seq(0.8,1.2,length=10),seq(1.2,3,length=10),'''

This will define the color range:

"red=[-1,0.8]

black=[0.8,1.2]

green=[1.2,3]"

[[Category:Protocols]]
[[Category:Metabolomics]]

==Run from text file==
'''Note: It is also possible to write all the steps in txt file as a single script.'''
===open the script ===
* In the file menu click open script
** Choose the proper directory and script file name
** The script file will be opened in the R Editor window
** If necessary changes can be made on the R Editor window

===run the script ===
* Click Run all or Run line or selection form the Edit menu

Making Heatmaps

2012-12-04T05:05:22Z

Teklab:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

heatmapname <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(heatmapname) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

heatmapname <- heatmapname [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

heatmapname_matrix <- data.matrix (heatmapname)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (heatmapname_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

'''Note: To rescale the color key, add break function to the heatmap.2. '''

'''breaks=c(seq(-1,0.8,length=10),seq(0.8,1.2,length=10),seq(1.2,3,length=10),'''

This will define the color range:

"red=[-1,0.8]

black=[0.8,1.2]

green=[1.2,3]"

[[Category:Protocols]]
[[Category:Metabolomics]]

'''It is also possible to write all the steps in txt file as a single script.'''
===open the script ===
*In the file menu click open script
**choose the proper directory and script file name
**the script file will be opened in the R Editor window
***If necessary changes can be made on the R Editor window

===To run the script===
* click Run all or Run line or selection form the Edit menu

Making Heatmaps

2012-12-04T05:04:18Z

Teklab:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

heatmapname <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(heatmapname) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

heatmapname <- heatmapname [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

heatmapname_matrix <- data.matrix (heatmapname)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (heatmapname_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

'''Note: To rescale the color key, add break function to the heatmap.2. '''

'''breaks=c(seq(-1,0.8,length=10),seq(0.8,1.2,length=10),seq(1.2,3,length=10),'''

This will define the color range:

"red=[-1,0.8]

black=[0.8,1.2]

green=[1.2,3]"

[[Category:Protocols]]
[[Category:Metabolomics]]

'''It is also possible to write all the steps in txt file as a single script.'''
===open the script ===
*In the file menu click open script
**choose the proper directory and script file name
**the script file will be opened in the R Editor window
***If necessary changes can be made on the R Editor window
===To run the script===
* click Run all or Run line or selection form the Edit menu

Making Heatmaps

2012-12-04T05:01:50Z

Teklab:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

heatmapname <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(heatmapname) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

heatmapname <- heatmapname [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

heatmapname_matrix <- data.matrix (heatmapname)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (heatmapname_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

'''Note: To rescale the color key, add break function to the heatmap.2. '''

'''breaks=c(seq(-1,0.8,length=10),seq(0.8,1.2,length=10),seq(1.2,3,length=10),'''

This will define the color range:

"red=[-1,0.8]

black=[0.8,1.2]

green=[1.2,3]"

[[Category:Protocols]]
[[Category:Metabolomics]]

'''It is also possible to write all the steps in txt file as a single script.'''
===open the script ===
= In the file menu click open script
=choose the proper directory and script file name
= the script file will be opened in the R Editor window
= If necessary changes can be made
=To run the script click Run all or Run line or selection form the Edit menu

Making Heatmaps

2012-12-04T05:01:22Z

Teklab:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

heatmapname <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(heatmapname) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

heatmapname <- heatmapname [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

heatmapname_matrix <- data.matrix (heatmapname)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (heatmapname_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

'''Note: To rescale the color key, add break function to the heatmap.2. '''

'''breaks=c(seq(-1,0.8,length=10),seq(0.8,1.2,length=10),seq(1.2,3,length=10),'''

This will define the color range:

"red=[-1,0.8]

black=[0.8,1.2]

green=[1.2,3]"

[[Category:Protocols]]
[[Category:Metabolomics]]

'''It is also possible to write all the steps in txt file as a single script.'''
= = =open the script = = =
= In the file menu click open script
=choose the proper directory and script file name
= the script file will be opened in the R Editor window
= If necessary changes can be made
=To run the script click Run all or Run line or selection form the Edit menu

Making Heatmaps

2012-12-04T05:01:07Z

Teklab:

==Load the data==
The data can be prepared in csv or text file to load the data in to R. For example, to load ''list.csv'':

heatmapname <- read.csv (“list.csv”)

==Name the rows==
You can then name the rows of the heatmap like so:

row.names(heatmapname) <- data$Name

To exclude the first column from the heat map, use a command of similar form to the following:

heatmapname <- heatmapname [,2: n]

In the above command, '''n''' is the number of columns to be included in the heat map.

==Build a data matrix==
Use the following command to build a data matrix for making the heat map:

heatmapname_matrix <- data.matrix (heatmapname)

==Plot the heat map==
'''Note: Gnuplot package must be installed in R before heat maps may be displayed!''' Run the following command to load in the ''gplots'' library.

library("gplots")

To make heat map, run the following command:

heatmap.2 (heatmapname_matrix, dendrogram="row", col= redgreen (75), scale="none",
key = TRUE, keysize = 1.0, margins = c(4,30),
density.info="none", trace="none")

'''Note: To rescale the color key, add break function to the heatmap.2. '''

'''breaks=c(seq(-1,0.8,length=10),seq(0.8,1.2,length=10),seq(1.2,3,length=10),'''

This will define the color range:

"red=[-1,0.8]

black=[0.8,1.2]

green=[1.2,3]"

[[Category:Protocols]]
[[Category:Metabolomics]]

'''It is also possible to write all the steps in txt file as a single script.'''
= =open the script = =
= In the file menu click open script
=choose the proper directory and script file name
= the script file will be opened in the R Editor window
= If necessary changes can be made
=To run the script click Run all or Run line or selection form the Edit menu

Vitamin C in Juices

2012-08-16T02:53:36Z

Teklab:

[[Category:Maxey Demos]]

==Experimentation with Vitamin C==
Determine the Vitamin C content in various freshly squeezed fruit juices. Compare kiwis and oranges (really high) to peaches or apples (really low). Or, blend a vegetable in water to create a solution that can be tested. You will want to use cheesecloth to remove the fiber from the solution. Fiber is a good for you too by the way. Bell peppers are particularly high in Vitamin C but the green ones are supposed to have higher content than the red or orange ones. The Natural Hub has we page that lists the Vitamin C content of many fruits at: http://www.naturalhub.com/natural_food_guide_fruit_vitamin_c.htm

===Materials===

#Fruit juices and fruit drinks containing vitamin C (use 1.00 mL per experiment)
#Vitamin C Standard solution (1 mg/mL)(use 1.00 mL per experiment)
#Starch solution (sue 1.00 mL per experiment and control for 2.00 mL total)
#Iodine solution (we actually make I3 - ; need up to 1.00 mL per experiment, so need 2.00 L)

===Procedure for fruit juice or drink===

#Carefully squirt 1.0 mL of fruit juice or drink into a 10-mL graduate cylinder
#Carefully squirt 1.0 mL of starch solution in to the same 10-mL graduated cylinder
#Empty the contents of the cylinder into a small Erlenmeyer flask.
#Use a pipet bulb to add the iodine solution.
;Count the number of drops it takes to form a purple color. :Swirl the flask to make sure the solution stays purple. If it doesn’t, add one more drop.
#Report your number of drops to the assistant.
#Repeat the procedure with the vitamin C standard

===Procedure for vitamin C standard===

#Carefully squirt 1.0 mL of vitamin C standard into a 10-mL graduated cylinder
#Carefully squirt 1.0 mL of starch solution into the same 10-mL graduated cylinder
#Empty the contents of the cylinder into a small Erlenmeyer flask.
#Use a pipet bulb to add the iodine solution.
;Count the number of drops it takes to form a purple color. :Swirl the flask to make sure the solution stays purple. If it doesn’t, add one more drop.
#Report your number of drops to the assistant.
#You can calculate the mg vitamin C from the following equation:
;(number of drops to fruit juice) / (number of drops to Vitamin C standard), recorded in mg.

The equation above has been simplified from this equation
Estimated Vitamin C content = (1 mL) x (1mg/mL) x (number of drops to fruit juice) / (number of drops to Vitamin C standard)