Question: (Closed) help with start DESeq
gravatar for batmaiden
4 months ago by
batmaiden0 wrote:


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 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!

rna-seq software error deseq • 249 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by batmaiden0

the question is solved

ADD REPLYlink written 4 months ago by batmaiden0

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.


PS: For line command Deseq2 usage help, please see
ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
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