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]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- [image: Benilton Carvalho on about.me] Benilton Carvalho about.me/benilton <http: about.me="" benilton=""> [[alternative HTML version deleted]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >