[BioC] AgiMicroRna problem

maryam shahmansoori [guest] guest at bioconductor.org
Sat Jan 26 13:48:41 CET 2013


hello
I get data(GSE37527) from GEO database and I am trying to analyze(normalize and identify DE) them in to R with package AgiMicroRna. Does my Data fit with this package. In my data doesn't exist the columns gMeanSignal and gBGUsed.
For my purpose which package is better than another. 
Please help me
thanks in advance









 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] AgiMicroRna_2.6.0     affycoretools_1.28.0  KEGG.db_2.7.1        
 [4] GO.db_2.7.1           RSQLite_0.11.2        DBI_0.2-5            
 [7] AnnotationDbi_1.18.4  preprocessCore_1.18.0 affy_1.34.0          
[10] limma_3.12.3          Biobase_2.16.0        BiocGenerics_0.2.0   

loaded via a namespace (and not attached):
 [1] affyio_1.24.0       annaffy_1.28.0      annotate_1.34.1    
 [4] BiocInstaller_1.4.9 biomaRt_2.12.0      Biostrings_2.24.1  
 [7] Category_2.22.0     gcrma_2.28.0        genefilter_1.38.0  
[10] GOstats_2.22.0      graph_1.34.0        grid_2.15.1        
[13] GSEABase_1.18.0     IRanges_1.14.4      lattice_0.20-6     
[16] RBGL_1.32.1         RCurl_1.95-3        splines_2.15.1     
[19] stats4_2.15.1       survival_2.36-14    tools_2.15.1       
[22] XML_3.95-0.1        xtable_1.7-0        zlibbioc_1.2.0   

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