[BioC] about citrus chip (update of xps)
cstrato at aon.at
Wed Sep 9 23:32:31 CEST 2009
Does someone has an explanation why Affymetrix has added probesets w/o
MMs to the Citrus.CDF file?
BTW, I have just uploaded a new version xps_1.4.9 (and xps_1.5.16) to
BioC which allows to do "mas5" and "mas5calls" for the Affymetrix Citrus
array by simply skipping the probesets w/o MMs.
e.m.a.i.l: cstrato at aon.at
James W. MacDonald wrote:
> Making any changes to mas5calls will be much less trivial than the
> background correction, and I don't have the time right now to spend on
> Your best bet is to use rma() and then filter on something like IQR.
> See the genefilter package for more options.
> yuduanding wrote:
>> hello Jim:
>> Sorry too trouble you again.After I installed affy package1.23.6 and
>> Biobase 2.5.6 the mas5 problem have solved.But I meet the similar
>> problems when run mas5calls and gcrma package on Citrus chips,I think
>> problem must be the NA in Citrus Chip,But I can find another way to
>> filtering out low quality data.
>> Here are the partial R codes :
>> AffyBatch object
>> size of arrays=984x984 features (16 kb)
>> cdf=Citrus (30395 affyids)
>> number of samples=1
>> number of genes=30395
>> background correction: mas PM/MM correction : mas expression values:
>> mas background correcting...done.
>> 30395 ids to be processed
>> #work well!!no problems!!
>> Getting probe level data...
>> Computing p-values
>> Error in FUN(1L[[1L]], ...) : NA/NaN/Inf in foreign function call
>> Adjusting for optical effect.Done.
>> Computing affinitiesLoading required package: AnnotationDbi
>> Error in matrix(NA, nrow = max(cbind(pmIndex,
>> mmIndex)), ncol = 1) :matrix: invalid 'nrow' value (too large or NA)
>> R version 2.9.1 (2009-06-26) x86_64-unknown-linux-gnu
>> attached base packages:
>>  stats graphics grDevices utils datasets methods base
>> other attached packages:
>>  citrusprobe_2.4.0 AnnotationDbi_1.6.1 gcrma_2.16.0 
>> Biostrings_2.12.8 IRanges_1.2.3 citruscdf_2.4.0 
>> affy_1.23.6 Biobase_2.5.6
>> loaded via a namespace (and not attached):
>>  affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0
>>  RSQLite_0.7-2 splines_2.9.1 tools_2.9.1
>> <jmacdon at med.umich.edu>" 2009-09-02 22:56:01
>> Re: RE James about mas5
>> The problem with running mas5 on the citrus chip is that there are 25
>> probesets that don't have any MM probes. Since the MM probes are used
>> for both background estimation/subtraction and computation of the
>> expression values this will be a problem for these probesets.
>> I have fixed the error you see in the devel version of affy, so if
>> you want to run mas5 on these data you need to upgrade to the devel
>> version of R, and then either get the corrected version of affy from
>> the svn server, or wait a day or two and use biocLite() to get it.
>> The version of the corrected affy package is 1.23.6.
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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