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

Hello,

I have a multiple time series RNA Sequencing data from this dataset https://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=ERX240756. And I want to format that data to be run in WGCNA as per instructions given here. https://wikis.utexas.edu/display/bioiteam/Clustering+using+WGCNA. 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

SRA_runtable.csv

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,

Prabath.

ADD COMMENTlink modified 6 weeks ago by Peter Langfelder1.3k • written 6 weeks ago by prab4th0
2
gravatar for Peter Langfelder
6 weeks ago by
United States
Peter Langfelder1.3k wrote:

Please read WGCNA FAQ at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html , especially points 3 and 4, but the rest my also be useful. Also, if you are new to WGCNA, please follow WGCNA tutorials at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html to get started (the lecture you linked to is based on the tutorials).

ADD COMMENTlink written 6 weeks ago by Peter Langfelder1.3k

Thank you!

[Variance Stabilizing Transformation](https://www.rdocumentation.org/packages/DESeq/versions/1.24.0/topics/varianceStabilizingTransformation) at this link helped.

I was surprised when l saw your name.

ADD REPLYlink written 6 weeks ago by prab4th0
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