Sorry for this maybe naive question, but I never analysed microarray before.
I'm trying to import .gpr files from a public dataset (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-104/) in limma thanks to the function read.maimages().
As specified in the documentation I've created a "target" file with the file names and the RNA information on cy3 and cy3, and implemented a function to filter flags, then I try to read the .gpr files that I've downloaded :
targets=readTargets("targets.csv",sep="\t", row.names="Name") f <- function(x) as.numeric(x$Flags > -49) RG <- read.maimages(files=targets$FileName,source="genepix",columns=list(R="GenePix:F635 Mean",G="GenePix:F532 Mean",Rb="GenePix:B635 Median",Gb="GenePix:B532 Median"), wt.fun=f)
Unfortunately I get the following error message :
Error in readGPRHeader(fullname) : File is not in Axon Text File (ATF) format
After some research I think it comes from the fact that the .gpr files have no headers. But I'm not really sure if it comes from that, and if it is the case, what "standard" header I could put to have the files imported.
If anyone has encountered the same issue and would advise me it would be really helpful.