Boxplot from GEO2R vs my own script

Question

[english.server]

Hi all!

I have downloaded the .cel files to GSE79326. The boxplot I draw is different from that drawn using GEO2R. I wondered why. My code is:

library (oligo)
afbatch=read.celfiles(list.celfiles()) 
dataset=exprs (rma (afbatch, normalize=F)) 
boxplot (dataset)

Thank you in advance.

[venu]

Don't you think if you show us two boxplots would be helpful to say what's happening there?

Answer 1

[Sean Davis]

The code for a GEO2R analysis is available from the GEO2R site. You might take a look at that code to see what GEO2R is doing that might be different.

One difference is that you are starting with .CEL files. GEO2R uses data as supplied by the submitter.