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

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