Question: Help with DEseq2 design matrix and DE expression analysis
0
gravatar for Naresh D J
4.0 years ago by
Naresh D J80
Turku/BTK
Naresh D J80 wrote:

Hi,

I am having 6 samples (A,B,C,D,E,F) each with two replicates. I have the HT-seq count table with raw read counts. I would like to do the DE analysis

A vs B

A vs C

A vs D

A vs E

A vs F

B vs C

B vs D...etc basically all the combinations of 1 sample vs other (in total 15 combinations). How can I do the this in DEseq2.

In addition, I would like to do the PCA and clustering on all 6 samples and would like to check whether replicates are similar in all samples and how similar the samples to each other.

Thank you very much.

Best Regards,

Naresh D J

rna-seq deseq2 • 1.3k views
ADD COMMENTlink modified 4.0 years ago by karl.stamm3.5k • written 4.0 years ago by Naresh D J80
1
gravatar for karl.stamm
4.0 years ago by
karl.stamm3.5k
United States
karl.stamm3.5k wrote:

There's a bioconductor package called rgsepd which has a function to do exactly what you are asking. You provide it a table of read counts, (column names are samples, row names are human RefSeq NM_###), and a second table of sample names to condition. Then it can do all pairs DESeq2 for you, filter the tables, generate PCAs, clustering and heatmaps.

See the manuals or ask a question, we can build a tutorial.

ADD COMMENTlink written 4.0 years ago by karl.stamm3.5k

Thanks you.

ADD REPLYlink written 4.0 years ago by Naresh D J80
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