Entering edit mode
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
> 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