Error ,when I use "pa.calls" function on my dataset
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@shamim-sarhadi-9395
Last seen 4.8 years ago

Hi everybody

I have merged two GSE with combat method, now I want to use panp package for selecting present genes in my merged eset and then downstream analysis... but I got an error that says:

> PA<-pa.calls(eset_COMBAT)
Error in AllExprs[NSMPnames, ] : subscript out of bounds
In addition: Warning messages:
1: In if (chip == "hgu133b") { :
 the condition has length > 1 and only the first element will be used
2: In if ((chip != "hgu133a") & (chip != "hgu133atag") & (chip != "hgu133plus2")) { :
  the condition has length > 1 and only the first element will be used
3: In if ((chip == "hgu133a") | (chip == "hgu133atag")) { :
  the condition has length > 1 and only the first element will be used

I have to say that my datasets platform are, HG-U133A  and HG-U133_Plus_2

 

 

panp Combat • 581 views
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> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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

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

other attached packages:
 [1] panp_1.40.0            affy_1.48.0            limma_3.26.9          
 [4] inSilicoMerging_1.14.0 inSilicoDb_2.6.0       RCurl_1.95-4.8        
 [7] bitops_1.0-6           Biobase_2.30.0         BiocGenerics_0.16.1   
[10] rjson_0.2.15           BiocInstaller_1.20.1  

loaded via a namespace (and not attached):
 [1] lattice_0.20-33       IRanges_2.4.8         Biostrings_2.38.4    
 [4] grid_3.2.4            stats4_3.2.4          zlibbioc_1.16.0      
 [7] XVector_0.10.0        affyio_1.40.0         latticeExtra_0.6-28  
[10] S4Vectors_0.8.11      preprocessCore_1.32.0 splines_3.2.4        
[13] RColorBrewer_1.1-2    gcrma_2.42.0          tools_3.2.4          
[16] affyPLM_1.46.0

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