How to analyze affy U133A micro-array data
Dear all,
I am new in genomics. I want to analyze the raw data in CellMiner, which is a data set of HG_U133A (version 2) of cancer cells. I have several problems to solve:
- How to convert/map X-Y positions in the .cel files to gene names?
- I can load .cel files by using ReadAffy() in R, but I don't know how/where to load the .cdf file? I found there are hgu133acdf,hgu133a2.db and hgu133a.db, I don't know how to choose and use them.
- For the further analysis, which package(s) in R are commonly used in a differential expression analysis? Is there any sample script I can follow for counting genes expressed in a .cel file?
Thank you very much for any help.
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have you checked this? Analysing Microarray Data In Bioconductor & http://jura.wi.mit.edu/bio/education/bioinfo2007/arrays/array_exercises_1R.html
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