Question: steps to get up and down regulated genes using DESeq2
0
gravatar for Tony
16 months 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 16 months ago by Michael Love25k • written 16 months ago by Tony0
Answer: steps to get up and down regulated genes using DESeq2
0
gravatar for Michael Love
16 months ago by
Michael Love25k
United States
Michael Love25k wrote:

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

ADD COMMENTlink written 16 months ago by Michael Love25k

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

ADD REPLYlink written 16 months 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 16 months ago by Michael Love25k

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

ADD REPLYlink written 16 months 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 16 months ago by Michael Love25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 254 users visited in the last hour