setting sizeFactors from scran :: caculateSumFactors.
1
0
Entering edit mode
OE • 0
@1b6d9c0f
Last seen 2.4 years ago
Morocco

Dear all,

I'm working on some data from scRNA-seq-based expermient in order to perform Differential Expression Analysis . I'm following the recommendations provided in DESeq2's vignette, but I still stuck with the step of setting sizeFactors from scran.

In fact, I calculated the size factors for all cells but my problem is I don't know how should I use them in the downstream steps.

Should I feed them to DESeq() or to results() , for instance, If so, how ? Because I searched in the arguments of these functions without finding any possibility to do that (to my limited knowledge of course).

Please give me some insights.

Thanks in advance !

scran DESeq2 • 1.1k views
ADD COMMENT
1
Entering edit mode
ATpoint ★ 4.5k
@atpoint-13662
Last seen 2 hours ago
Germany

You can conveniently convert your SingleCellExperiment to a DESeqDataSet, see https://bioconductor.org/packages/devel/bioc/vignettes/scran/inst/doc/scran.html#8_Converting_to_other_formats, which makes sure your size factors end up in the right slot of the new object. I think you only have to set a design then using design(dds) <- ~whatever+you:want.

ADD COMMENT

Login before adding your answer.

Traffic: 708 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6