Hi all,

My 3' QuantSeq counts matrix has been summarized and imported with tximport (txi$counts) and contains non-integer values, causing problems with DESeqDataSetFromMatrix.

Code:

txi <- tximport(files = files, type="salmon", tx2gene = transcripts, countsFromAbundance = "no")
targets <- read.table('design.csv', sep=',', header=TRUE)
condition <- factor(targets$condition)
df <- txitx$counts
df <- df[, rownames(targets)]
dds <- DESeqDataSetFromMatrix(df, targets, ~condition) #per recommendation from the vignette

Upon which DESeq2 returns

Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

...which is true due to the nature of tximport, but the vignette cautions against length correction from DeSeqDataSetFromTximport (which doesn't complain about the above command). I set "countsfromAbundance" to "no" and so all values in the resulting "length" vector were set to 100; will the function still correct for length?

Thanks for your input!

You should round() the counts before providing to DESeqDataSetFromMatrix.