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Question: RankProd throws "is.infinite(data)" error for type "S4" for differential expression analysis
1
gravatar for Tina Chapman
4 months ago by
Tina Chapman20
Tacoma, WA
Tina Chapman20 wrote:

Hi, I am having a problem using RankProd on Windows 10. All packages involved are updated to the most recent version. I also apologize if this is an easy fix—I am an undergraduate student and a new user. I'm using RankProd, Affy, and Limma.

I am running a small batch of sample data (6 .CEL files, 3 replicates for both WT and the control) in RankProd in order to become acquainted with the package, and I am getting an error while running RP.out. “Error in is.infinite(data) : default method not implemented for type 'S4'”.

It is also interesting because I have a PC, tried it on a different PC, and a Mac desktop. It works on the Mac but not on either PC, where I get the same error on both devices.

Here is the code that I am running:

> abatch.raw <- ReadAffy() 
> targets <- readTargets("affy_targets.txt") 
> data<-ReadAffy(filenames=targets$FileName) 
> eset<-rma(data) 
> write.exprs(eset, file="normdata.txt") 
> n1<-3 
> n2<-3 
> cl<-rep(c(0,1),c(n1,n2)) 
> origin<-rep(1,n1+n2) 
> arab.sub<-eset[,which(origin==1)] 
> arab.cl.sub<-cl[which(origin==1)] 
> arab.origin.sub<-origin[which(origin==1)] 
> RP.out <- RP(arab.sub,arab.cl.sub, num.perm=100, logged=TRUE, na.rm=FALSE, plot=FALSE, rand=123) 
Rank Product analysis for unpaired case 
Error in is.infinite(data) : default method not implemented for type 'S4'

My tab delimited .txt file, “affy_targets.txt” is as follows (the formatting didn't copy over, but it looks good!):

Name FileName Target WT 1 No0_43.CEL WT 1 WT 2 No0_59.CEL WT 2 WT 3 No0_60.CEL WT 3 fbs1 1 fbs1_45.CEL fbs1 1 fbs1 2 fbs1_61.CEL fbs1 2 fbs1 3 fbs1_62.CEL fbs1 3

Any guidance would be greatly appreciated! I’m not sure if this is something that I’m doing wrong, or if it is some sort of new bug. Again, it's strange because it is working on the Mac, but not on either PC, even when running identical commands.

Below is my sessionInfo(). Thanks for your help.

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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] RankProd_3.2.0      Rmpfr_0.6-1         gmp_0.5-13.1        limma_3.32.2       
[5] affy_1.54.0         Biobase_2.36.2      BiocGenerics_0.22.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11          AnnotationDbi_1.38.1  zlibbioc_1.22.0      
 [4] IRanges_2.10.2        bit_1.1-12            rlang_0.1.1          
 [7] blob_1.1.0            tools_3.4.0           DBI_0.7              
[10] bit64_0.9-7           digest_0.6.12         tibble_1.3.3         
[13] preprocessCore_1.38.1 affyio_1.46.0         S4Vectors_0.14.3     
[16] memoise_1.1.0         RSQLite_2.0           compiler_3.4.0       
[19] BiocInstaller_1.26.0  stats4_3.4.0      
ADD COMMENTlink modified 4 months ago by James W. MacDonald45k • written 4 months ago by Tina Chapman20
1
gravatar for James W. MacDonald
4 months ago by
United States
James W. MacDonald45k wrote:

I don't see anywhere in the code (or the help page) where you can input anything but a matrix to RP or RankProducts. Does

RP.out <- RP(exprs(arab.sub),arab.cl.sub, num.perm=100, logged=TRUE, na.rm=FALSE, plot=FALSE, rand=123)

work for you?

ADD COMMENTlink written 4 months ago by James W. MacDonald45k
1

Yes, this works. I thought that eset returned a matrix. Thanks for the fix!

ADD REPLYlink written 4 months ago by Tina Chapman20
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