Question: using Limma to read 2-channel dye-swap in Agilent scanner
7.5 years ago by
Neta • 10
Neta • 10 wrote:
Hello, I am using Limma (version 3.12.0) to read 2-channel dye-swap files from an Agilent image analysis scanner, where each sample has 2 files - one for cy3 and one for cy5. However, the only reference to such a 2-file input in the limma user guide is to "ImaGene". When I try to read the files and the target file using the following commands: RG = read.maimages(file_names, ...) targets = readTargets("targets.txt") files = targets[,c("FileNameCy3","FileNameCy5")]; RG = read.maimages(files,source="imagene"); I get the following error message: Error in read.imagene(files = files, path = path, ext = ext, names = names, : Can't find Field Dimensions in ImaGene header In addition: Warning message: In readImaGeneHeader(fullname) : End of file encountered before End Header When I try to use source="Agilent" instead of "imagene", the command doesn't seem to understand that I have 2 file names, and gives the following error message: Error in read.maimages(files, source = "agilent") : targets frame doesn't contain FileName column I tried every single option for "source" that was listed in the help of "read.maimages" but it seems like "imagene" is the only one that is able to digest the two headers for the file names. I am stuck and would appreciate any help. Thank you, Neta.
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