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Daedalus99
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@daedalus99-20694
Last seen 5.6 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
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