[BioC] GSVA questions

Joe [guest] guest at bioconductor.org
Fri Sep 6 02:45:41 CEST 2013


 I'm a GSVA package new user. One question make me confused. If I used custom CDF (download from BrainArray website), usually, the custom CDF file has unique ProbeID correspond to one gene, so this format expression data could be used in GSVA?
Another one, exclude c2BroadSet, is there any GeneSellection data could be used or download? 

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] genefilter_1.42.0              primeviewhsentrezgprobe_17.1.0
 [3] primeviewhsentrezg.db_17.1.0   org.Hs.eg.db_2.9.0            
 [5] RSQLite_0.11.4                 DBI_0.2-7                     
 [7] primeviewhsentrezgcdf_17.1.0   AnnotationDbi_1.22.6          
 [9] Biobase_2.20.1                 BiocGenerics_0.6.0            
[11] rj_1.1.3-1                    

loaded via a namespace (and not attached):
[1] annotate_1.38.0 IRanges_1.18.3  rj.gd_1.1.3-1   splines_3.0.1  
[5] stats4_3.0.1    survival_2.37-4 tools_3.0.1     XML_3.98-1.1   
[9] xtable_1.7-1   

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