Entering edit mode
Sim, Fraser
▴
350
@sim-fraser-2871
Last seen 10.0 years ago
Hi-
I have a quick question relating to the use of annotation packages in
Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D,
E
chips. I have performed RMA and generated expression data for each
chip
type individually and then used rbind to make a single matrix with all
the data. I can use limma just fine to then perform differential gene
analysis.
I would like to use additional functions such as GO Hyper G testing
but
I couldn't find an annotation package that combined all 5 chips. How
would I go about generating a new annotation package that combined the
five individual annotation packages? Or how should I approach this
problem?
Thanks,
Fraser
SessionInfo:
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] splines stats graphics grDevices datasets utils tools
methods base
other attached packages:
[1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0
gdata_2.4.2 gtools_2.5.0
[6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0
annaffy_1.12.1 KEGG.db_2.2.0
[11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0
RCurl_0.9-3 GOstats_2.6.0
[16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0
xtable_1.5-2 GO.db_2.2.0
[21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4
graph_1.18.1 limma_2.14.5
[26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2
preprocessCore_1.2.0 affyio_1.8.0
[31] Biobase_2.0.1
loaded via a namespace (and not attached):
[1] cluster_1.11.10 XML_1.94-0.1
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