I have downloaded GSE file through R and unzip these files to extract CEL files. Now I want to read these cel files by using readAffy function for that purpose I am using commands 1. library(affy) # to load library 2. raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="Genechip") but this returns me an error mentioned below Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, : object 'cels' not found what should I do know? Am I using correct commands?Please guide me.
I can see two errors.
cdfname="Genechip". cdfname should be the name of the R cdf file for the specific type of Affymetrix array the data comes from. But you don't usually need to specify the name of the file, if you omit this parameter R should find the right cdf file automatically.
filenames=cels. You can omit the filenames parameter if all the files in your working directory are cel files, and you want ReadAffy to read all of them, otherwise you should supply a vector with the names of all the cel files you want it to read.
See the vignette for the Bioconductor affy package,
If you go to the vignette I gave a link to above, on page 8 they work through an example with a dataset named Dilution, from the affydata package. If you work through their example code, it will give you an idea of how the functions in the affy package work, what kind of output to expect when they are running, and how to know when the code completes successfully.