Hi,
I want to analyze my RNA-seq data in DESeq2. I have the following code:
library( "GenomicFeatures" ) hse <- makeTxDbFromGFF( "~/Homo_sapiens.GRCh38.92.gtf", format="gtf" ) exonsByGene <- exonsBy( hse, by="gene" )
fls <- list.files( "./", pattern="bam$", full=TRUE )
library( "Rsamtools" ) bamLst <- BamFileList( fls, yieldSize=100000 )
library( "GenomicAlignments" ) se <- summarizeOverlaps( exonsByGene, bamLst, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE )
library( "DESeq2" )
sampleInfo <- read.csv( "sample.csv" ) sampleInfo <- DataFrame( sampleInfo ) seIdx <- match(colnames(se), sampleInfo$run)
colData(se) <- cbind( colData(se), sampleInfo)
ddsFull <- DESeqDataSet( se, design= ~FALSE )
countdata <- assay(se) coldata <- colData (se)
ddsFullCountTable <- DESeqDataSetFromMatrix( countData = countdata, colData = coldata, design = ~ FALSE)
dds <- ddsFullCountTable as.data.frame( colData(dds) )
dds <- DESeq(dds, betaPrior = FALSE)
And function DESeq gives an error: Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
Help me, please!
the question is solved
Hello batmaiden!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!