Dahlquist:Microarray Data Analysis Workflow: Difference between revisions
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=== Running the Normalization Scripts === | === Running the Normalization Scripts === | ||
* Create a folder on your Desktop to store your files for the microarray analysis procedure. | |||
* Download the [https://lionshare.lmu.edu/Users/kdahlqui/SURP%202015/wt-dCIN5-dGLN3-dHAP1-dHMO1-dSWI4-dZAP1-Spar_gpr-files.zip zipped file] that contains the <code>.gpr</code> files and move it to this folder. | |||
** Unzip this file using 7-zip. Right-click on the file and select the menu item, "7-zip > Extract Here". | |||
* Download the [https://lionshare.lmu.edu/Users/kdahlqui/SURP%202015/GCAT_Targets.csv GCAT_Targets.csv] file and [https://lionshare.lmu.edu/Users/kdahlqui/SURP%202015/Ontario_Targets_wt-dCIN5-dGLN3-dHAP4-dHMO1-dSWI4-dZAP1-Spar_20150514.csv Ontario_Targets_wt-dCIN5-dGLN3-dHAP4-dHMO1-dSWI4-dZAP1-Spar_20150514.csv] files and move them to this folder. | |||
=== Creating MA and box plots === | === Creating MA and box plots === |
Revision as of 14:18, 15 May 2015
This is the most current version of the data analysis protocol for the Dahlquist Lab microarray data. We will perform this analysis as a group during Week 1 of SURP 2015.
Summary of steps for microarray data analysis
- Quantitate the fluorescence signal in each spot (GenePix Pro)
- Calculate the ratio of red/green fluorescence (GenePix Pro)
- Log transform the ratios (GenePix Pro)
- Normalize the ratios on each microarray slide (within-chip normalization)
- Normalize the ratios for a set of slides in an experiment (between-chip normalization)
- Perform statistical analysis on the ratios
- Within-strain ANOVA
- Modified t test for each timepoint
- Between-strain ANOVA
- Benjamini & Hochberg and Bonferroni p value corrections for the above three tests
- "Sanity Check" on above three tests
- Pattern finding algorithms (clustering with stem)
- Gene Ontology term enrichment analysis (on clusters with stem or on gene sets with MAPPFinder)
- Pathway analysis (GenMAPP)
- Determining candidate transcription factors and gene regulatory network (YEASTRACT)
- Dynamical modeling with GRNmap; visualization with GRNsight
Steps 1-3: Generating Log2 Ratios with GenePix Pro
- The protocol for gridding and generating the intensity (log2 ratio) data with GenePix Pro 6.1 is found on this page.
- This protocol will generate a
*.gpr
file for each chip which is then fed into the normalization protocol below.
Steps 4-5: Within- and Between-chip Normalization
- A more detailed protocol can be found on this page. An abbreviated protocol is summarized below.
Installing R 3.1.0 and the limma package
The following protocol was developed to normalize GCAT and Ontario DNA microarray chip data from the Dahlquist lab using the R Statistical Software and the limma package (part of the Bioconductor Project).
- The normalization procedure has been verified to work with version 3.1.0 of R released in April 2014 (link to download site) and and version 3.20.1 of the limma package ( direct link to download zipped file) on the Windows 7 platform.
- Note that using other versions of R or the limma package might give different results.
- Note also that using the 32-bit versus the 64-bit versions of R 3.1.0 will give different results for the normalization out in the 10-13 or 10-14 decimal place. The Dahlquist Lab is standardizing on using the 64-bit version of R.
- To install R for the first time, download and run the installer from the link above, accepting the default installation.
- To use the limma package, unzip the file and place the contents into a folder called "limma" in the library directory of the R program. If you accept the default location, that will be C:\Program Files\R\R-3.1.0\library (this will be different on the computers in S120 since you do not have administrator rights).
Running the Normalization Scripts
- Create a folder on your Desktop to store your files for the microarray analysis procedure.
- Download the zipped file that contains the
.gpr
files and move it to this folder.- Unzip this file using 7-zip. Right-click on the file and select the menu item, "7-zip > Extract Here".
- Download the GCAT_Targets.csv file and Ontario_Targets_wt-dCIN5-dGLN3-dHAP4-dHMO1-dSWI4-dZAP1-Spar_20150514.csv files and move them to this folder.