Question: DESeqFromMatrix for 3'end data via tximport; non-integer values
0
gravatar for cats_dogs
4 months ago by
cats_dogs20
cats_dogs20 wrote:

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!

deseq2 tximport • 118 views
ADD COMMENTlink modified 4 months ago by Michael Love23k • written 4 months ago by cats_dogs20
Answer: DESeqFromMatrix for 3'end data via tximport; non-integer values
0
gravatar for Michael Love
4 months ago by
Michael Love23k
United States
Michael Love23k wrote:

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

ADD COMMENTlink written 4 months ago by Michael Love23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 144 users visited in the last hour