Question: (Closed) Basemean always multiples of 0.5 in deseq2 results
gravatar for batmaiden
4 months ago by
batmaiden0 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,
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(, 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!

basemean rna-seq deseq2 results • 130 views
ADD COMMENTlink written 4 months ago by batmaiden0

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

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
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