Hi.
On Mon, Mar 19, 2012 at 12:02 PM, Fong <fongchunc...@gmail.com> wrote:
> Hi,
>
> I am using SNP6 arrays right now and I've got an annotationData directory
> that looks like this:
>
> GenomeWideSNP_6,Full.cdf
> GenomeWideSNP_6,Full,monocell.CDF
> GenomeWideSNP_6,HB20080710.acs
> GenomeWideSNP_6,Full,na24,hg18,HB20080214.ugp
> GenomeWideSNP_6,Full,na24,hg18,HB20080214.ufl
> GenomeWideSNP_6,Full,na26,hg18,HB20080821.ugp
> GenomeWideSNP_6,Full,na26,hg18,HB20080821.ufl
>
> Essentially I have the na24 and na26 .ugp and .ufl files. Now when I run
> the code:
>
> library('aroma.affymetrix')
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>
> print(gi)
>
> UgpGenomeInformation:
> Name: GenomeWideSNP_6
> Tags: Full,na24,hg18,HB20080214
> Full name: GenomeWideSNP_6,Full,na24,hg18,HB20080214
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na24,hg18,HB20080214.ugp
> File size: 8.97 MB (9407568 bytes)
> RAM: 0.00 MB
> Chip type: GenomeWideSNP_6,Full
>
> It seems to always look for the first .ugp file which ends up being the
> na24.
Yes, it returns the first matching UGP file, where it search files in
lexicographic ("alphabetic+numeric") order.
> I've tried to give it tags by going
>
> gi <- getGenomeInformation(cdf, tags='Full,na26,hg18,HB20080821')
That argument 'tags' will be ignored. I'll add it to the to do list,
to see if it should/could be supported.
>
> But it still defaults to na24. Is there a way to keep the annotation files
> in the same directory, but tell aroma.affymetrix to use a different set of
> annotation files for SNP6 arrays?
You can do as follows:
library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
gi <- UgpGenomeInformation$byChipType(getChipType(cdf),
tags="na31,hg19,HB20110328");
setGenomeInformation(cdf, gi);
such that getGenomeInformation(cdf) returns what you wish.
Hope this helps
/Henrik
>
> Thanks,
>
> Fong
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
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>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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