Entering edit mode
Hongxian He
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20
@hongxian-he-261
Last seen 10.3 years ago
Today I independently identified a bug in the pmcorrect.mas method
from
"affy" package (v1.1.1), which has been posted on the mailing list
before.
But I found that the bug is still in the lastest release of affy
package,
and the results computed therefore disagree with MAS5.
pm.corrected <- applycbindpps.pm, pps.im, delta), 1, max)
{
...
pm.corrected <- applycbindpps.pm, pps.im, delta), 1, max)
...
}
Shouldn't the above line be
pm.corrected <- applycbindpps.pm - pps.im, delta), 1, max)
according to the formula V_{i,j} = max(PM_{i,j} - IM_{i,j}, d) in
Affymetrix statistical algorithm document, where PV_{i,j}=
log2(V_{i,j}),
PV_{i,j} is the probe value for probe pair j in probeset i?
Thanks,
Hongxian He
Center of Bioinformatics
University of Pennsylvania
==================================================================
Quoted from the archive:
[BioC] the result of bioconductor not agree with MAS
"H?sing, Johannes" johannes.huesing at medizin.uni-essen.de
Mon Mar 10 18:04:43 MET 2003
> -----Original Message-----
> From: Ben Bolstad [mailto:bolstad at stat.berkeley.edu]
> Sent: Thursday, March 06, 2003 5:48 PM
> To: Lang Chen
> Cc: 'bioconductor at stat.math.ethz.ch'
> Subject: Re: [BioC] the result of bioconductor not agree with MAS
>
>
> Hi Lang Chen (and to anyone else this is an issue for),
>
> We have made our best attempts to duplicate the MAS 5.0
> algorithm using
> available documentation.
If I read the code in pmcorrect.mas() correctly (affy version 1.1),
the mismatch is not subtracted from the perfect match, so the line
pm.corrected <- applycbindpps.pm, pps.im, delta), 1, max)
should IMHO rather read
pm.corrected <- applycbindpps.pm-pps.mm, pps.im-pps.mm, delta), 1,
max) ?
I might very well be missing something, so if somebody could give
me a clue I'd be grateful.
Best regards
Johannes
