[BioC] question about package AgiMicroRna

maryam shahmansouri [guest] guest at bioconductor.org
Tue Aug 20 14:14:09 CEST 2013

1)I need that to implement another normalization between arrays methods like GPA and vsn,LVS,CyclicLoess on the ddTGS(gTotalGeneSignal).
2)I am interest that to obtain an estimate of the gene signal using the RMA algorithm without the function rmaMicroRna ; First I read data into RGlist,then I get BG corrected  and normalized between arrays in limma, but I don't know how can to obtain the median of the replicated probes. 
Please help me.

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

[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] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] LVSmiRNA_1.6.0        vsn_3.24.0            MASS_7.3-23          
 [4] quantreg_5.02         SparseM_1.03          AgiMicroRna_2.6.0    
 [7] affycoretools_1.28.0  KEGG.db_2.7.1         GO.db_2.7.1          
[10] RSQLite_0.11.4        DBI_0.2-7             AnnotationDbi_1.18.4 
[13] preprocessCore_1.18.0 affy_1.34.0           limma_3.12.3         
[16] 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_0.20-21    
[16] RBGL_1.32.1         RCurl_1.95-4.1      stats4_2.15.1      
[19] survival_2.37-4     tools_2.15.1        XML_3.98-1.1       
[22] xtable_1.7-1        zlibbioc_1.2.0   

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