converting counts to integer mode
Error in validObject(.Object) :
invalid class “DESeqDataSet” object: NA values are not allowed in the count matrix
In addition: Warning message:
In `mode<-`(`*tmp*`, value = c(395L, 231L, 243L, 866L, 3L, 45L, :
NAs introduced by coercion
I have check in my count matrix there is no NA values. Probably you can give me some suggestion about this problem. Thank you.
Just to restate, DESeq2 is designed for gene-level analysis, and we recommend using software such as htseq-count, summarizeOverlaps or featureCounts to obtain for each gene a count of fragments which can be uniquely aligned to that gene.
"Many of the read count from htseq was 0 because this ambiguity."
I'm not sure exactly what problem you are describing, but if you want to sum all the reads/fragments for a gene family, you could edit the annotation file so that these genes all make up one feature. However if you want to test each gene in the family separately, it is not recommended as input to DESeq(2) to use non-uniquely assigning reads. You can search the archive to find many posts on this topic.