[BioC] Package oligo: Transcript level P/A calls
cstrato
cstrato at aon.at
Sun Aug 10 23:55:11 CEST 2014
Dear Kavitha,
Alternatively, you could use package xps, which does allow you to make
P/A calls at both probeset and transcript levels for Mouse gene ST 1.0
arrays, see function dabg.call().
In addition, package xps has implemented MAS5 in a way that does also
support whole genome and exon arrays, see function mas5().
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l: cstrato at aon.at
_._._._._._._._._._._._._._._._._._
On 8/7/14 9:17 PM, Mukund, Kavitha wrote:
> Hello All,
>
> I am trying to make P/A calls at both probeset and transcript levels for Mouse gene ST 1.0 array using Oligo.
>
> Here is what I did for probeset level P/A calls
>
> mmNormal_ps <- rma(mmNormal_raw, target="probeset")
> dabgPS <- paCalls(mmNormal_raw, "PSDABG")
> ind <- apply(dabgPS, 1, function(x) sum(x < 0.01) > 5)
> mm_ps <- mmNormal_ps[ind,]
>
> But I have been unable to implement it at a transcript level, say,
>
> mmNormal <- rma(mmNormal_raw, target="core") #transcript level
> dim(mmNormal) # Features 35556 Samples 12
>
> Clearly, I can't do
> dabg<- paCalls(mmNormal_raw, "DABG") # Probe level
> dim(dabg) # 899636 12
>
> And it doesn't work when I try and do
> Mas5<- paCalls(mmNormal_raw, "MAS5") # I guess because mmNormal_raw is a GeneFeatureSet object.
>
> Can anyone tell me what I am missing when implementing transcript level paCalls using Oligo? I have made P/A calls on affybatch objects but haven't used oligo. Any help/pointers in this regard is much appreciated.
> Thank you in advance.
>
> -Kavitha
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.4 DBI_0.2-7
> [4] oligo_1.28.2 Biostrings_2.32.0 XVector_0.4.0
> [7] IRanges_1.22.9 oligoClasses_1.26.0 limma_3.20.8
> [10] Biobase_2.24.0 BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.36.0 affyio_1.32.0 BiocInstaller_1.14.2
> [4] bit_1.1-12 codetools_0.2-8 ff_2.2-13
> [7] foreach_1.4.2 GenomeInfoDb_1.0.2 GenomicRanges_1.16.4
> [10] iterators_1.0.7 preprocessCore_1.26.1 splines_3.1.0
> [13] stats4_3.1.0 tools_3.1.0 zlibbioc_1.10.0
>
> [[alternative HTML version deleted]]
>
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