Question: (Closed) Basemean always multiples of 0.5 in deseq2 results
4 months ago by
batmaiden • 0
batmaiden • 0 wrote:
I analyzing RNA-seq with two samples: control and treatment. I use the following sequence of software: sortmerna -> hisat2 -> DESeq2. This is my R code for DESeq2:
library( "GenomicFeatures" ) hse <- makeTxDbFromGFF( "~/Homo_sapiens.GRCh38.92.gtf", format="gtf" ) trans <- transcriptsBy( hse, by="gene" ) fls <- list.files( "./", pattern="bam$", full=TRUE ) library( "Rsamtools" ) bamLst <- BamFileList( fls, yieldSize=100000 ) library( "GenomicAlignments" ) se <- summarizeOverlaps( trans, bamLst, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE ) library( "DESeq2" ) sampleInfo <- read.csv( "sample.csv" ) sampleInfo <- DataFrame( sampleInfo ) seIdx <- match(colnames(se), sampleInfo$run) colData(se) <- cbind( colData(se), sampleInfo) ddsFull <- DESeqDataSet( se, design= ~run ) countdata <- assay(se) coldata <- colData (se) ddsFullCountTable <- DESeqDataSetFromMatrix( countData = countdata, colData = coldata, design = ~run) dds <- ddsFullCountTable dds <- DESeq(dds) res <- results( dds ) write.csv( as.data.frame(res), file="results.csv" )
Everything works, but there is a problem with the results: all values in the column "Basemean" are multiples of 0.5 (apparently some setting). What parameters need to be changed? Thank you so much!
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