I would like to know
how can I do to read binary.CEL.gz files
because R sends an error like this
Error in read.affybatch(filenames = l$filenames, phenoData =
l$phenoData, :
Is
/affylims/genechip/lots/VAGIN_29-04-05/gcos_files/R006-05FX7Z08C1-R1.C
EL.gz
really a CEL file? tried reading as text, gzipped text and binary
Execution halted
is there some treack that I can use
other than use gunzip?
On Friday 29 September 2006 14:59, D.Enrique ESCOBAR ESPINOZA wrote:
> I would like to know
> how can I do to read binary.CEL.gz files
> because R sends an error like this
> Error in read.affybatch(filenames = l$filenames, phenoData =
> l$phenoData, :
> Is
> /affylims/genechip/lots/VAGIN_29-04-05/gcos_files/R006-05FX7Z08C1-R1
.CEL.gz
> really a CEL file? tried reading as text, gzipped text and binary
> Execution halted
You might check the file sizes of .CEL files of the same chip. You
can get
this error if the .CEL file is corrupted in some way.
Sean
Sean Davis wrote:
> On Friday 29 September 2006 14:59, D.Enrique ESCOBAR ESPINOZA wrote:
>
>>I would like to know
>>how can I do to read binary.CEL.gz files
>>because R sends an error like this
>>Error in read.affybatch(filenames = l$filenames, phenoData =
>>l$phenoData, :
>> Is
>>/affylims/genechip/lots/VAGIN_29-04-05/gcos_files/R006-05FX7Z08C1-R1
.CEL.gz
>>really a CEL file? tried reading as text, gzipped text and binary
>>Execution halted
>
>
> You might check the file sizes of .CEL files of the same chip. You
can get
> this error if the .CEL file is corrupted in some way.
And if they really are gzipped binary celfiles, you will have to unzip
them first. As the error says, ReadAffy() only reads in text, binary,
and gzipped _text_ celfiles.
Best,
Jim
>
> Sean
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
As others have mentioned: gzipped binary format cel files are
currently
not supported.
However, gzipped text format cel files are supported and are treated
as
first class citizens (ie handled automatically and can be mixed with
text and binary format files in the same batch).
There is no reason why this couldn't also true for gzipped binary
format
files. Up until now there has been no demand for this which is why it
has not been implemented.
Best,
Ben
On Fri, 2006-09-29 at 11:59 -0700, D.Enrique ESCOBAR ESPINOZA wrote:
> I would like to know
> how can I do to read binary.CEL.gz files
> because R sends an error like this
> Error in read.affybatch(filenames = l$filenames, phenoData =
> l$phenoData, :
> Is
> /affylims/genechip/lots/VAGIN_29-04-05/gcos_files/R006-05FX7Z08C1-R1
.CEL.gz
> really a CEL file? tried reading as text, gzipped text and binary
> Execution halted
>
> is there some treack that I can use
> other than use gunzip?
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Ben Bolstad <bmb at="" bmbolstad.com="">
http://bmbolstad.com
