I'm trying to use this data for differential expression analysis. I would like to use the processed data, which seems like it is the .cel file at the supplementary file. On top of that, there's also a data table shown. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM496105
I just have a few question about this. 1. Is the data table a preview of what is in the .cel file? 2. According to data processing, it seems like the content of .cel was already normalized. I was wondering when I get the .cel file, if I just go straight to the analysis. If so, I can't quite figure out how to do that. I used affy package in R:
a = justRMA(filenames = "ctrl_1.CEL", normalize = FALSE, background = FALSE ) write.exprs(a,file="evals.txt")
and the head of the output is https://imgur.com/4v8FSbH (in the first pic) as opposed to in the second pic, which is from geo page.
Please help me understand what is going on and what to do. Thank you all in advance!