[BioC] how to put together 600 files from the 5.0 Affy SNPchip
Laura Rodriguez Murillo
laura.lmurillo at gmail.com
Fri Nov 7 18:04:02 CET 2008
Thank you for your reply. I had tried with this software but it
doesn't recognize my files, it looks as it doesn't like .txt files.
2008/11/6 David Carter <dcarter at robarts.ca>:
> Hi Laura,
> Affymetrix has a free tool (free and easy to download) called Genotyping
> Console that will export 1 file for all your samples with SNPs on rows and
> samples on columns. I haven't tried it with 622 samples though...
> David Carter
> Laura Rodriguez Murillo wrote:
>> I'm new in this mailing list and also using bioconductor. I'd
>> appreciate your feedback on this: I have 622 files that correspond to
>> 622 samples genotyped for the SNPs in the 5.0 SNPChip from Affymetrix.
>> Each file consists of two columns of almost 500 K rows (plus 4 lines
>> at the begining that I won't need). The number of rows are the same in
>> every file. I would need to put all these files together, where the
>> first column is common to all of them (SNP names) (so I just need it
>> once in the big file). Once I have all the columns one after the other
>> I would also need to paste a column with the chromosome number for
>> each SNP (which is in another file, just this info alone). Do you know
>> if there's any way to do this with Bioconductor?.
>> Thank you!
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives:
> David Carter
> Facility Manager
> London Regional Genomics Centre
> Robarts Research Institute, Room 4.01
> PO Box 5015, 100 Perth Drive
> London, Ontario, Canada, N6A 5K8
> phone: 519-663-3253
> fax: 519-663-3037
> dcarter at robarts.ca
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