I have a *.txt file which contains microarray expression data only. Each row corresponds to a probe, and each column to a sample. I know the data has not been normalized and would like to normalize it using the rma() function in affy. I've tried simply importing the data using read.table(), but when I then try to apply the rma() function to the data, this gives the following error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘probeNames’ for signature ‘"matrix"’
I believe the way to avoid this error would be to somehow read the data into an AffyBatch, since the rma() function needs an AffyBatch as the input. How would you go about reading a *.txt file in to an AffyBatch? Alternatively, is there some way to apply the rma() function to a matrix/data.frame?
Thanks in advance!