Question: Reading CEL files using Oligo and pd.hta.2.0 packages in Windows 7
0
gravatar for ladhikari
2.1 years ago by
ladhikari0
ladhikari0 wrote:

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 windows 7 R cel pd.hta.2.0 • 533 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by ladhikari0
Answer: Reading CEL files using Oligo and pd.hta.2.0 packages in Windows 7
0
gravatar for James W. MacDonald
2.1 years ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 2.1 years ago by James W. MacDonald51k
Answer: Reading CEL files using Oligo and pd.hta.2.0 packages in Windows 7
0
gravatar for ladhikari
2.1 years ago by
ladhikari0
ladhikari0 wrote:

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.

 

ADD COMMENTlink written 2.1 years ago by ladhikari0
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