Cannot read CEL files

Question

[Microuser]

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")
affyRaw <- read.celfiles(celFiles)

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!

Answer 1

[Kevin Blighe]

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

1. your current working directory
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