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Question: steps to get up and down regulated genes using DESeq2
0
gravatar for Tony
12 weeks ago by
Tony0
Tony0 wrote:

Which are the steps to get significantly up regulated and down regulated genes from samples which are not replicates?

By doing this step "dds <- DESeq(dds)" I am getting a warning message "same number of samples and coefficients to fit..."

 

Is it possible to get different combination results? The input will be multiple samples read count in a single file.

 

ADD COMMENTlink modified 12 weeks ago by Michael Love19k • written 12 weeks ago by Tony0
0
gravatar for Michael Love
12 weeks ago by
Michael Love19k
United States
Michael Love19k wrote:

Replicates are required to test for significance of up and down DE.

ADD COMMENTlink written 12 weeks ago by Michael Love19k

Okay. Which are the steps we have to use to get up regulated and down regulated genes?

ADD REPLYlink written 12 weeks ago by Tony0

Please take a look at our workflow:

http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

ADD REPLYlink written 12 weeks ago by Michael Love19k

Is there any difference between old DESeq and DESeq2 in calculating the up and down regulated genes?

ADD REPLYlink written 12 weeks ago by Tony0
1

This is answered in our papers and specifically in the vignette, see the Table of Contents. Please take some time to read over our documentation before posting. I want to focus my time on support questions not covered in the publications and documentation.

ADD REPLYlink written 12 weeks ago by Michael Love19k
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