Transcriptomics data analysis
Arrayanalysis.org derived R packages for affymetrix micro arrays
How to use: Open affyAnalysisQC.R - these are the settings - what plots are required, plotted, customisable, copy together with the data Adapt: DATA.DIR - directory where the CEL files can be found SCRIPT.DIR - where the scripts (run, functions, affy are) WORK.DIR - where to put the output
prefOligo - prefer oligo over affy (standard, no need to change) arrayGroup = add link to description file - no symbols or numbers for group name start, make sure to add .txt or .CEL to the filenames Example CEL file name sample name group Bla.CEL 1 group1 BLa1.CEL 2 group2
save
run the affyAnalysisQC.R