[BioC] about citrus chip
James W. MacDonald
jmacdon at med.umich.edu
Tue Sep 8 17:26:01 CEST 2009
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 that.
Your best bet is to use rma() and then filter on something like IQR. See
the genefilter package for more options.
> 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)
> 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.
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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