I am using the HISAT, Stringtie, and Ballgown pipeline to do transcriptome expression analysis. So far I went through these steps.
bg=ballgown(dataDir=data_directory, samplePattern='1and2', meas='all') bg_ifungis = ballgown(dataDir = data_directory, samplePattern = '1and2', pData=pheno_data) bg_ifungis_filt = subset(bg_ifungis,"rowVars(texpr(bg_ifungis)) >1",genomesubset=TRUE) results_transcripts = stattest(bg_ifungis_filt, feature="transcript",covariate="timepoint",adjustvars = c("location"), getFC=TRUE, meas="FPKM")
So here, I set adjustvars to the location column in my pData, which is either Earth or ISS. However, here I have compared all of Earth samples to all of ISS, and now I would like to compare each separately, on their own.
I first tried changing the
results_transcripts code to this
results_transcripts_E = stattest(bg_ifungis_filt, feature="transcript",covariate="timepoint",adjustvars = c("location=Earth"), getFC=TRUE, meas="FPKM")
Did not work, said Earth is not a valid covariate. Then I tried to subset the data using ballgowns subset command
bg_ifungis_Earth = subset(pheno_data,"pheno_data$location == Earth",genomesubset=FALSE) > Error in subset.data.frame(pheno_data, "pheno_data$location == Earth", : 'subset' must be logical
I tried variations of the above, but kept getting a similar error. Is there any way I can subset my data by location in Ballgown? Or am I going to have to re-do the Stringtie assemblies and everything so that Earth and ISS are treated separately?
I hope that makes sense!
Thanks in advance, Morgan