I would like to learn more about certain "mystery" transcript clusters that pop up when I analyze Mouse Gene 2.0 ST data.
Brief summary: I use the oligo package to summarize at the transcript level, then I get rid of everything but the main array content with Jim MacDonald's suggestion:
annot <- pData(netaffxTranscript)
ind <- annot$category %in% "main"
esetfiltered <- eset[ind,]
Finally, I use Limma to do group comparisons. Some probe sets that come up in my differentially expressed genes are a puzzle to me though. One example would be "17290922". According to mogene20sttranscriptcluster.db, this probe set does not map to any accession numbers (none at all?). When I search for it in Affy's MoGene-2_0-st-v1.na33.mm10.transcript.csv file, it is not listed. NetAffx returns no hits, but instead directs me to the page of transcript cluster 17290921, where at the bottom of the page I am informed that 17290922 is a "related" exon probe set. So it seems to me that it should not even exist on my array. I checked in the annotation for MoGene 2.1, and on that chip, the 17290922 probe set seems to be an intronic control. But I am sure I am working with MoGene 2.0 (as my CEL files say so).
I am very curious to learn more, could somebody perhaps give a pointer? Thanks so much in advance.
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)
attached base packages:
 parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
 limma_3.22.7 pd.mogene.2.0.st_2.14.1
 oligo_1.30.0 Biostrings_2.34.1
 XVector_0.6.0 oligoClasses_1.28.0
 mogene20sttranscriptcluster.db_8.2.0 org.Mm.eg.db_3.0.0
 RSQLite_1.0.0 DBI_0.3.1
 AnnotationDbi_1.28.2 GenomeInfoDb_1.2.4
 IRanges_2.0.1 S4Vectors_0.4.0
 Biobase_2.26.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
 affxparser_1.38.0 affyio_1.34.0 BiocInstaller_1.16.2 bit_1.1-12
 codetools_0.2-11 ff_2.2-13 foreach_1.4.2 GenomicRanges_1.18.4
 iterators_1.0.7 preprocessCore_1.28.0 splines_3.1.3 zlibbioc_1.12.0