Question: RNAseq differential expression analysis : learning design matrix
3
gravatar for guillaume.rbt
7 weeks ago by
guillaume.rbt530
France
guillaume.rbt530 wrote:

Hi all,

I'm a bioinformatician and I often have to deal with RNAseq differential gene expression analysis projects.

I think I understand well the whole process to get from the raw data to the the normalized read counts but, unfortunately, due to my little statistical background, I'm having trouble dealing with the last step of differential expression.

When it comes to simple pairwise comparison between two conditions I understand the process, but when there is more complex comparisons (timelapses, multiple comparisons, including confounding effect ... ) I'm struggling for chosing the relevant design matrices.

I'm curious if anyone would know good tutorials, online courses, books, or any ressources that would allow me to learn how to get better at that.

Thank for your help,

ADD COMMENTlink modified 7 weeks ago by i.sudbery4.1k • written 7 weeks ago by guillaume.rbt530
2

Try reading the limma and edgeR user's guides. They were written for not statistician audience.

ADD REPLYlink written 7 weeks ago by b.nota6.4k
1

I was also searching for such a guide. I ended up reading a lot of Q&A in DESeq2 support forum, they're usually well explained and written by Mike, DESeq2 developer.

ADD REPLYlink written 7 weeks ago by Asaf5.3k

Yes that is also what I usually do when I'm stuck, it is really helpful !

ADD REPLYlink written 7 weeks ago by guillaume.rbt530
3
gravatar for i.sudbery
7 weeks ago by
i.sudbery4.1k
Sheffield, UK
i.sudbery4.1k wrote:

I've not actually done it myself, but people say good things about Rafael Irizarry's courses. Particularly see weeks 3 and 4 of the Introduction to Linear Models and Matrix Algebra course here and chapter 5 of his book.

ADD COMMENTlink written 7 weeks ago by i.sudbery4.1k

Thank for the tip, I will look into it :)

ADD REPLYlink written 7 weeks ago by guillaume.rbt530
1

I have gone through these courses and these actually provide a solid intuition behind the same.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by noorpratap.singh260
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