Question: number of genes for co-expression network
0
gravatar for Edalat
3.0 years ago by
Edalat30
Edalat30 wrote:

Hi, I did differential expression by DEseq2 for some coding and lncoding RNAseq data,this is my summery result of DEseq2 by adjusted p-value < 0.1:

for lncoding:

out of 26998 with nonzero total read count

adjusted p-value < 0.1

LFC > 0 (up) : 10, 0.037%

LFC < 0 (down) : 13, 0.048%

outliers [1] : 241, 0.89%

low counts [2] : 11375, 42%

(mean count < 1)

and for coding:

out of 19933 with nonzero total read count

adjusted p-value < 0.1

LFC > 0 (up) : 335, 1.7%

LFC < 0 (down) : 300, 1.5%

outliers [1] : 289, 1.4%

low counts [2] : 6012, 30%

(mean count < 61)

as you see I have 23 genes for lncoding ad 635 genes for coding after filtering,this number of genes is OK for making co-expression network?

rna-seq deseq2 co-expression • 788 views
ADD COMMENTlink modified 3.0 years ago by shunyip180 • written 3.0 years ago by Edalat30
1
gravatar for shunyip
3.0 years ago by
shunyip180
shunyip180 wrote:

You can draw a co-expression network with just two genes. If you do not set a correlation threshold, you will have a network with 2 nodes and 1 edge.

Since you have 658 genes, which will give you a maximum of around 200k edges, you can try out different thresholds to decrease the number of edges. I suggest that you should try out different thresholds to see if your network is fine. Whether it is OK or not depends on your data and your experiment.

I hope this helps.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by shunyip180
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 2.3.0
Traffic: 2369 users visited in the last hour