[BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays
MarÃa Maqueda [guest]
guest at bioconductor.org
Fri Nov 29 12:18:50 CET 2013
I am analyzing a set of Affymetrix Human Gene 2.0 ST arrays, this is my first time working with this type of arrays so I have a few general questions. I would very much appreciate any advice you could give.
(1) I have obtained different lists of differentially expressed genes (using eBayes() from limma). In those lists, some control transcripts are popping up (i.e normgene -> intron category among other categories). I was not expecting this type of transcripts at this point. In theory after normalization, no control transcripts should appear, am I right? Have you experienced this?
I have read that one possibility is to use getMainProbes before topTable selection but I wonder if there could be something wrong from the beginning with my normalization process (I have used rma() â transcript level - from oligo). What is your opinion?
(2) This type of arrays also includes lincRNA transcripts and I am interested in considering them for my analysis. The thing is that I am using hugene20sttranscriptcluster.db for annotation and these lincRNA are not included. Would this library be able to handle them?
(3) I tried to make my own annotation package thru makeDBPackage based on .csv annotation file from Affy but I got an errorâ¦: Error in `[.data.frame`(csvFile, , GenBank IDName) : undefined columns selected
I have already read in this mailing list that makeDBPackage may expect a HGU133plus2 annotation âstyleâ. Would the library annotationForge be able to handle this?
Many thanks in advance for any help!
Biomedical Engineering Research Centre (CREB)
Universitat PolitÃ¨cnica de Catalunya (UPC)
-- output of sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 human.db0_2.9.0 AnnotationForge_1.2.2
 hugene20sttranscriptcluster.db_2.12.1 org.Hs.eg.db_2.9.0
 AnnotationDbi_1.22.6 BiocInstaller_1.12.0
 limma_3.16.8 pd.hugene.2.0.st_3.8.0
 oligo_1.24.2 Biobase_2.20.1
 oligoClasses_1.22.0 BiocGenerics_0.6.0
 RSQLite_0.11.4 DBI_0.2-7
loaded via a namespace (and not attached):
 affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0
 Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8
 ff_2.2-12 foreach_1.4.1 genefilter_1.42.0
 GenomicRanges_1.12.5 IRanges_1.18.4 iterators_1.0.6
 preprocessCore_1.22.0 splines_3.0.1 stats4_3.0.1
 survival_2.37-4 tools_3.0.1 XML_3.98-1.1
 xtable_1.7-1 zlibbioc_1.6.0
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