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Entering edit mode
22 months ago
Microuser • 0

Hi,

I want to reanalyze some of microarray data on GEO database. I typed the following codes for at least 2 different entries (different GSEs), but get the error message that the files do not exist. I am new to this type of analysis, anyone can suggest me any solution please?

getGEOSuppFiles("GSE15936")
untar("GSE15936/GSE15936_RAW.tar")
cels = list.files("data", pattern = "CEL")
sapply(paste("data", cels, sep="/"), gunzip)
celFiles <- list.celfiles("data")

Error: These do not exist:
GSM399864.CEL
GSM399865.CEL
GSM399870.CEL
GSM399871.CEL
GSM399872.CEL


If I don't unzip the .gz files, I still have the same problem and no affyRaw will be made.

Thank you!

microarray cel • 1.3k views
2
Entering edit mode
22 months ago

Hey, you should always be aware of 2 things when programming:

2. the contents of all of the objects in your workspace

You may solve your issue by checking the output of getwd() and also checking the contents of all objects that you create with the above code.

I think that the following will work, though:

affyRaw <- read.celfiles(list.files(path = 'data/',
pattern = '*.CEL$', full.names = TRUE))  So, please note the difference between the following two commands: list.celfiles("data") list.files(path = 'data/', pattern = '*.CEL$', full.names = TRUE)


Kevin