Entering edit mode
Hi,
I'm hoping to use "tximport" to convert an RNA-Seq count data file for downstream analysis such as DESeq2. But I got an error as you can see below. I think everything I have is current (R3.3.1 etc). Any input will be much appreciated !!
> datafileName <- "test.txt" ## Replace the file name with the correct one
> table=read.delim(datafileName,header=T)
>
> countsCol=colnames(table[,4:11])
> abundanceCol=colnames(table[,12:ncol(table)])
> RefSeqID=table[,3]
> Symbol=table[,2]
> tx2gene = data.frame(RefSeqID,Symbol)
> txin = tximport(datafileName, type="none", tx2gene = tx2gene, countsCol = countsCol,
+ abundanceCol=abundanceCol, lengthCol=NULL, txIdCol=NULL,
+ importer = read_tsv)
reading in files
1 Error in .subset2(x, i, exact = exact) :
attempt to select less than one element in get1index
Thank you very much for quick reply. I was trying to find a solution to my problem with DESeqDataSetFromMatrix(). I tried but it did not take a matrix as you can see below. Only way so far was to put count columns without the row name column (in this case Symbol). What am I doing wrong?
> datafileName <- "test.txt" ## Replace the file name with the correct one > table=read.delim(datafileName,header=T) > > table=as.matrix(table[,c(2,5:12)]) ## column2 is "GeneSymbol";columns 5-12 are raw counts > head(table) Symbol MEF258 MEF258OHT MEF284 MEF284OHT MEF285 MEF285OHT MEF286 MEF286OHT [1,] "BC021785" " 0" " 4" " 0" " 0" " 0" " 0" " 0" " 1" [2,] "Eea1" " 3756" " 3527" " 4339" " 3835" " 3951" " 3831" " 3619" " 5891" [3,] "Adgrg6" " 5887" " 5151" " 4659" " 3134" " 4463" " 5453" " 3299" " 6849" [4,] "Osbpl8" " 5712" " 7739" " 9810" " 10208" " 3767" " 4675" " 2923" " 6016" [5,] "Ttc41" " 15" " 42" " 24" " 25" " 10" " 36" " 19" " 65" [6,] "Mars" " 6214" " 4115" " 4704" " 2539" " 5166" " 5006" " 4325" " 8964" > > cellid <- rep( c("1", "2", "3", "4"), each=2) > cellid=as.factor(cellid) > treatment=rep(c(0, 1), 4) > condition=as.factor(treatment) > condition=relevel(condition, ref="0") > meta = data.frame(cellid, condition) > meta cellid condition 1 1 0 2 1 1 3 2 0 4 2 1 5 3 0 6 3 1 7 4 0 8 4 1 > > d <- DESeqDataSetFromMatrix(countData=table, colData = meta, design = ~condition) Error in `rownames<-`(`*tmp*`, value = c("Symbol", "MEF258", "MEF258OHT", : invalid rownames lengthSorry! I found a solution myself for the input for DESeqDataSetFromMatrix(). Simple matrix didn't work, but adding rownames to a count-data-only table solved it.
Thanks for taking time for your reply!
You got it. countData should be only a matrix of counts.
The correct error message was not coming through due to some recent code additions.
I've fixed the error message in the next version to say:
Error: ncol(countData) == nrow(colData) is not TRUE