Hi All,

In the Deseq2 vignette the first step is creating the object 

dds <- DESeqDataSet(se, design = ~ batch + condition)

based on the RangedSummarizedExperiment object se.

In my case, I have a raw count expression matrix (that I got from Kallisto) stored in "exp" and the metadata stored in "met".

I used the following code without creating  RangedSummarizedExperiment object:

mydds <-DESeqDataSetFromMatrix(countData = ecp,colData = met,design = ~batch+condition)

Is mydds == dds?

Thanks!

that is correct. try str(dds ) from the example and than also str(mydds) from your data and see if they have the same strucutre.

but to make your life easier Michael Love already created a package to import Kallisto data into DESeq2. A: Count matrix from Kallisto as input for DESeq2