Question: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
0
gravatar for lirongrossmann
22 months ago by
lirongrossmann40 wrote:

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!

ADD COMMENTlink modified 22 months ago • written 22 months ago by lirongrossmann40

is your count data stored in exp or ecp?

 

ADD REPLYlink written 22 months ago by Assa Yeroslaviz1.4k

exp.... sorry for the typo

ADD REPLYlink written 22 months ago by lirongrossmann40
Answer: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
0
gravatar for Assa Yeroslaviz
22 months ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k wrote:

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

ADD COMMENTlink modified 22 months ago • written 22 months ago by Assa Yeroslaviz1.4k

Thank you! 

Does it matter if I use the count matrix I have  (the one I got from Kallisto) with Deseqdatafrommatrix instead of tximport? My understanding is that I need to use tximport if I have transcript abundance estimates, but I have reads counts per genes, i.e. counts of reads aligned to a gene. 

Would it make any difference in terms of the DEG I got?

Thanks 

ADD REPLYlink modified 22 months ago • written 22 months ago by lirongrossmann40
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