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   


	[[alternative HTML version deleted]]

