I'm trying to perform a DE analysis on NanoString data. Using NanoStringDiff 1.16 I can get the example data that comes with the package to run in ~10 minutes following the package vignette:
> directory <- system.file("extdata", package="NanoStringDiff", mustWork=TRUE) > path<-paste(directory,"Mori.csv",sep="/") > designs=data.frame(group=c("Normal","Normal","Tumor","Tumor")) > NanoStringData=createNanoStringSetFromCsv(path,header=TRUE,designs) > pheno=pData(NanoStringData) > group=pheno$group > design.full=model.matrix(~0+group) > contrast=c(-1,1) > NanoStringData=estNormalizationFactors(NanoStringData) > result=glm.LRT(NanoStringData1,design.full,contrast=contrast)
However, when I load my own data, all steps run (and based on the output appear to run correctly) until I get to the final command:
> designs=data.frame(group=c("Control","Control","Group1","Group1")) > NanoStringData=createNanoStringSetFromCsv(mydata.csv,header=TRUE,designs) > pheno=pData(NanoStringData) > group=pheno$group > design.full=model.matrix(~0+group) > contrast=c(-1,1) > NanoStringData=estNormalizationFactors(NanoStringData) > result=glm.LRT(NanoStringData,design.full,contrast).
It hangs without producing any output. I gave it 20 hours before I had to kill it. Any ideas what could be making it take so long?
I have re-checked the formatting of my input data and it matches exactly what is detailed in the vignette (a csv count table with the three first columns being "Code.Class", "Name", and "Accession". I have also tried this with versions 1.16 and 1.14 of NanoStringDiff and I have tried it on both Windows and Linux platforms.
My dataset has 768 features and 15 samples so I didn't think it should take much longer than the example.
Is there perhaps a verbose option to get some progress output from the glm.LRT command?