Dear Kavitha,

I'm unaware of P/A calls at the transcript level. Could you please point me
to some references so I can add it to my TODO list and future versions of
oligo?

At this moment, you get calls at the probe and probeset (as defined in the
PGF file) levels:

da1 = paCalls(<obj>, 'DABG')
da2 = paCalls(<obj>, 'PSDABG')
probes = pm(<obj>, level='probeset')
probesets = rma(<obj>, level='probeset')
dim(da1)
dim(probes)
dim(probeset)
dim(da2)

And, you're correct, MAS5 isn't defined for Gene ST arrays.

benilton


2014-08-07 16:17 GMT-03:00 Mukund, Kavitha <kmukund@ucsd.edu>:

> 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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>



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[image: Benilton Carvalho on about.me]

Benilton Carvalho
about.me/benilton
  <http://about.me/benilton>

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