Question: (Closed) Basemean always multiples of 0.5 in deseq2 results
0
batmaiden • 0 wrote:
Hi,
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!
Hello batmaiden!
We believe that this post does not fit the main topic of this site.
This forum focuses on Galaxy usage. A better place to ask this question is https://support.bioconductor.org/.
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