maryam shahmansouri [guest] | 20 Aug 14:14 2013

question about package AgiMicroRna


Hello
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.
Thanks

 -- output of sessionInfo(): 

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