How to analyze affy U133A micro-array data

Question

[husince]

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:

1. How to convert/map X-Y positions in the .cel files to gene names?
2. 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.
3. 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.

Answer 1

[lessismore]

have you checked this? Analysing Microarray Data In Bioconductor & http://jura.wi.mit.edu/bio/education/bioinfo2007/arrays/array_exercises_1R.html

[husince]

Thank you for your reply. They are useful documents.