Analyzing (HiSeq) PANCAN data set RNA-seq data using DaMiRseq
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Daedalus99 • 0
@daedalus99-20694
Last seen 4.9 years ago

I'm trying to import two .csv files. One a class type and the other count data. I have been using the DaMiRseq import instructions listed as follows:

library(DaMiRseq)

rawdata.path <- ("C:/TCGA-PANCAN-HiSeq-801x20531/") filecounts <- list.files(rawdata.path, full.names = TRUE)[2] filecovariates <- list.files(rawdata.path, full.names = TRUE)[1] countdata <- read.delim(filecounts) covariatedata <- read.delim(filecovariates)

However when i attempt to

SE<-DaMiR.makeSE(countdata, covariatedata)

I receive the error "Error in DaMiR.makeSE(countdata, covariatedata) : the count data is not numeric" Any help would be appreciated.

Instructions are listed in https://bioconductor.org/packages/release/bioc/vignettes/DaMiRseq/inst/doc/DaMiRseq.pdf

DaMiR RNA-seq software error DaMiRseq • 885 views
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Dear Daedalus, sorry for the delay. Probably, the notification of your post ended up in my SPAM. Regarding your problem, I think that your countdata file is not well formatted. I guess because of one of these two reasons: 1) some elements of the count matrix are not integer; 2) countdata has some non-numeric extra-columns.

BTW, you can also generate SE, by the 'SummarizedExperiment' function (DaMiR.makeSE is actually a wrapper of this function). Best regrads, Mattia

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