Reading CEL files using Oligo and pd.hta.2.0 packages in Windows 7
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ladhikari • 0
@ladhikari-13851
Last seen 3.9 years ago

Hi all,

I am new to Bioconductors and I am trying to read some set of CEL files using Oligo package in R:

source("https://bioconductor.org/biocLite.R")
biocLite("oligo")
biocLite("pd.hta.2.0")

library(oligo)
library(pd.hta.2.0)

celFiles <- list.celfiles(full.names=TRUE)
affyRaw <- read.celfiles(celFiles)

Unfortuntely, the read.celfiles(celFiles) line gives me the following error:

Error: These are not readable: ./GSM1487519_TreatedChip9.CEL

My R and Bioconductor configurations are

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

and 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help

Note: However, if I use the exact same R 3.4.1 and Bioconductor 3.5 in Mac, I can read the same CEL files using pd.hta.2.0 without any errors. 

Any suggestions/comments are welcome. 

Thanks!

 

oligo pd.hta.2.0 CEL R windows 7 • 846 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 23 hours ago
United States

The error you see comes from this test:

## must be readable
  readable <- file.access(filenames, 4) == 0
  if (any(!readable)){
    msg <- paste("These are not readable:",
                 paste("\t", filenames[!readable], collapse="\n"), sep="\n")
    stop(msg, call.=FALSE)
  }

Where the test is to see if R has read permission for the files, and R is saying that it does not. Windows doesn't seem to be as strict about things like read bits (like e.g., Linux), but instead seems to worry more about whether or not a file is already being accessed by another process. So it might be that for whatever reason that particular file was 'in use' and you need to free it up.

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Entering edit mode
ladhikari • 0
@ladhikari-13851
Last seen 3.9 years ago

Thanks James for your quick response! 

I just figured out that there is a permission problem in our shared folders. It works if the CEL files are in local C: drive.

 

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