Question: Normalised counts of control samples in gene expression matrix
1
gravatar for Pranavathiyani G
19 months ago by
Pondicherry, India
Pranavathiyani G290 wrote:

I have 4 control and 4 treated samples of RNA seq data, for generating gene expression network should i consider adding the normalised counts of control samples in the gene expression matrix?

ADD COMMENTlink modified 19 months ago by Devon Ryan93k • written 19 months ago by Pranavathiyani G290

You are supposed to calculate DEGs or Statistically significant genes between two groups (control vs treated) using methods of your choice (in general people use scientific community accepted packages such as ballgown, DESeq2, EdgeR etc). For this analysis, you would need raw counts than normalized counts. Then one can plot expression networks. Just with one group (in tihs case control samples), it doesn't make sense to me, to arrive at expression networks.

ADD REPLYlink written 19 months ago by cpad011212k
2
gravatar for Devon Ryan
19 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

Yes, you would tend to include all of the group when making a coexpression network. You need larger sample numbers to make a reliable network anyway, so you can only achieve that by including all of your samples.

ADD COMMENTlink written 19 months ago by Devon Ryan93k
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