[BioC] Yeast 2.0 Arrays

[James W. MacDonald]

Hi Mike,

On 7/8/2010 8:40 AM, Mike Walter wrote:
> Hi there,
>
> I have a question on Affymetrix Yeast 2.0 arrays. These arrays
> contain about 5000 probesets for budding and fission yeast,
> respectively. We hybridized budding yeast sample and now I'd like to
> get rid of all the fission yeast probes before normalization. There
> is a mask file outlining which probesets belong to which organism.
> However, when I use ReadAffy(..., rm.mask=T) the number of probes
> does not change (s. below). Is there a way to specify a mask file
> during the affybatch import?

I assume you are using the mask file when scanning the chip?

If so, the probes for fission yeast should all be NA, which your test 
below will not detect (having a bunch of NA probes won't affect the 
dimension of your pm matrices). Something like

pms <- pm(d1, LISTRUE = TRUE)

length(pms) - sum(sapply(pms, function(x) all(is.na(x)))

or now that I think about it,

apply(pm(d1), 2, function(x) sum(!is.na(x)))

should give you a measure of how many non NA probesets remain.

Best,

Jim


>
> Any hints are welcome.
>
> Mike
>
>> d1<- ReadAffy(celfile.path=celfile, filenames=filenames,
>> rm.mask=F) d2<- ReadAffy(celfile.path=celfile, filenames=filenames,
>> rm.mask=T) dim(pm(d1))
> [1] 120855      5
>> dim(pm(d2))
> [1] 120855      5
>> sessionInfo()
> R version 2.10.1 (2009-12-14) i386-pc-mingw32
>
> locale: [1] LC_COLLATE=German_Germany.1252
> LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252
> LC_NUMERIC=C [5] LC_TIME=German_Germany.1252
>
> attached base packages: [1] stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages: [1] yeast2cdf_2.5.0      affyQCReport_1.24.0
> lattice_0.18-3 [4] RColorBrewer_1.0-2   affyPLM_1.22.0
> preprocessCore_1.8.0 [7] xtable_1.5-6         simpleaffy_2.22.0
> gcrma_2.18.1 [10] genefilter_1.28.2    affy_1.24.2
> Biobase_2.6.1
>
> loaded via a namespace (and not attached): [1] affyio_1.14.0
> annotate_1.24.1     AnnotationDbi_1.8.2 [4] Biostrings_2.14.12
> DBI_0.2-5           grid_2.10.1 [7] IRanges_1.4.16      RSQLite_0.9-1
> splines_2.10.1 [10] survival_2.35-8     tools_2.10.1
>>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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