Question

Reading CEL files

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Entering edit mode

libya.tahani • 0

@libyatahani-9206

Last seen 8.2 years ago

Libyan Arab Jamahiriya

Hi all,

I have a problem during I try to read CEL files ReadAffy() , my code was:

> data<-ReadAffy()
Error in read.celfile.header(as.character(filenames[[1]])) : 
  Is C:/Users/SONY/Documents/myproject/CEL/~$M187272.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats

And

> sessionInfo() 

R version 3.2.2 (2015-08-14)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1



locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          

[5] LC_TIME=English_United States.1252    



attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     



other attached packages:

[1] affy_1.48.0          Biobase_2.30.0       BiocGenerics_0.16.1  BiocInstaller_1.20.3



loaded via a namespace (and not attached):

[1] zlibbioc_1.16.0       tools_3.2.2           affyio_1.40.0         preprocessCore_1.32.0

Any advice please?

Regards.

Tahani.H

cel affy • 1.6k views

ADD COMMENT • link updated 8.2 years ago by James W. MacDonald 67k • written 8.2 years ago by libya.tahani • 0

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Entering edit mode

Have a look at the error message, it points to a file ~$M187272.CEL whose name looks like a temporary file generated by a Windows application. Try removing it, and generally please clean up the directory so that it only contains valid CEL files.

You can also give the names of the CEL files to ReadAffy() directly, this a more robust way to call that function.

ADD REPLY • link 8.2 years ago Wolfgang Huber ★ 13k

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Entering edit mode

Hi Wolfgang Huber , thank you for your answer . I really did what you did explain above , but it still giving an error !!

> data<-ReadAffy()
Error in read.celfile.header(as.character(filenames[[1]])) : 
  Is C:/Users/SONY/Documents/myproject/CEL1/GSM187268.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats

Even I put the CEL files in a separated folder and remove all other files !!!

> getwd()
[1] "C:/Users/SONY/Documents/myproject/CEL1"
> list.celfiles()
 [1] "GSM187268.CEL" "GSM187269.CEL" "GSM187271.CEL" "GSM187272.CEL" "GSM187273.CEL" "GSM187274.CEL" "GSM187275.CEL" "GSM187276.CEL" "GSM187277.CEL" "GSM187278.CEL"

How can I give the names of the CEL files to ReadAffy() directly according to my CEL files above , please?

Regards.

Tahani.H

ADD REPLY • link 8.2 years ago libya.tahani • 0

score 1 · Answer 1 · 2016-09-19

Most likely you have one or more corrupted files, which you could figure out by trying to read each one individually. But do note that the authors who submitted those data used RMA in R, so unless you want to do some other normalization/summarization (and there is very little profit in doing so), you can just use getGEO in the GEOquery package to get the summarized data directly, without having to bother with the raw data.