Question

steps to get up and down regulated genes using DESeq2

0

Entering edit mode

Tony • 0

@tony-15866

Last seen 6.5 years ago

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.

deseq2 without replicate no replicates • 3.4k views

ADD COMMENT • link updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by Tony • 0

score 0 · Answer 1 · 2018-05-21

0

Entering edit mode

Michael Love 43k

@mikelove

Last seen 6 days ago

United States

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

ADD COMMENT • link 6.5 years ago Michael Love 43k

0

Entering edit mode

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

ADD REPLY • link 6.5 years ago Tony • 0

0

Entering edit mode

Please take a look at our workflow:

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

ADD REPLY • link 6.5 years ago Michael Love 43k

0

Entering edit mode

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

ADD REPLY • link 6.5 years ago Tony • 0

1

Entering edit mode

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 REPLY • link 6.5 years ago Michael Love 43k