Question: How to get an output from DESeq2 to be used in WGCNA package
gravatar for prab4th
12 months ago by
prab4th0 wrote:


I have a multiple time series RNA Sequencing data from this dataset And I want to format that data to be run in WGCNA as per instructions given here. It requires normalized counts from DESeq2

I used salmon to quantify the FASTQ data and then I used the salmon output as an input in DESeq2 to get the normalized counts and this was the result I got.

> summary(res)
out of 32190 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)     : 1, 0.0031%
LFC < 0 (down)   : 1, 0.0031%
outliers [1]     : 0, 0%
low counts [2]   : 10, 0.031%
(mean count < 0)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
> head(res)
log2 fold change (MLE): condition saline vs control
Wald test p-value: condition saline vs control
DataFrame with 6 rows and 6 columns
               baseMean log2FoldChange      lfcSE       stat     pvalue      padj
              <numeric>      <numeric>  <numeric>  <numeric>  <numeric> <numeric>
OS01G0100100 738.209551    -0.17673172 0.09758808 -1.8109970 0.07014131 0.9273344
OS01G0100200   2.574911     0.23633606 0.69610387  0.3395126 0.73422358 0.9999039
OS01G0100300   1.899514    -0.50248710 0.84652268 -0.5935896 0.55278661 0.9999039
OS01G0100400  60.627709     0.12229393 0.19781440  0.6182256 0.53642663 0.9999039
OS01G0100500 598.837423     0.03060639 0.07374455  0.4150326 0.67811806 0.9999039
OS01G0100600 306.945725    -0.04714581 0.10914117 -0.4319709 0.66576255 0.9999039

But the WGCNA package requires the data to be in the form of gene name and the normalized counts for each sample. What should I change in my DESeq2 procedure to get an output like that.

DESeq2 code


Library_Name_s, Run_s nippon_control_1hr_rep1 extract,ERR266228

nippon_control_1hr_rep2 extract,ERR266233 nippon_control_1hr_rep3 extract,ERR266230

nippon_control_5hr_rep1 extract,ERR266229 nippon_control_5hr_rep3 extract,ERR266222

nippon_control_5hr_rep2 extract,ERR266223 nippon_control_24hr_rep1 extract,ERR266225

nippon_control_24hr_rep2 extract,ERR266234 nippon_control_24hr_rep3 extract,ERR266232

nippon_salt_1hr_rep1 extract,ERR266237 nippon_salt_1hr_rep2 extract,ERR266236 nippon_salt_1hr_rep3 extract,ERR266235 nippon_salt_5hr_rep1 extract,ERR266227 nippon_salt_5hr_rep2 extract,ERR266224

nippon_salt_5hr_rep3 extract,ERR266221 nippon_salt_24hr_rep1 extract,ERR266238

nippon_salt_24hr_rep2 extract,ERR266226 nippon_salt_24hr_rep3 extract,ERR266231

How I got the tx2gene.csv

I would be happy to provide more details.

Thank you,


ADD COMMENTlink modified 12 months ago by Peter Langfelder1.6k • written 12 months ago by prab4th0
gravatar for Peter Langfelder
12 months ago by
United States
Peter Langfelder1.6k wrote:

Please read WGCNA FAQ at , especially points 3 and 4, but the rest my also be useful. Also, if you are new to WGCNA, please follow WGCNA tutorials at to get started (the lecture you linked to is based on the tutorials).

ADD COMMENTlink written 12 months ago by Peter Langfelder1.6k

Thank you!

[Variance Stabilizing Transformation]( at this link helped.

I was surprised when l saw your name.

ADD REPLYlink written 12 months ago by prab4th0

Hi Peter,

Can you please send link for this tutorial as it is not available now?

ADD REPLYlink written 4 weeks ago by sbbinfo900
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