Question: Normalised counts of control samples in gene expression matrix
gravatar for Pranavathiyani G
5 months ago by
Pondicherry, India
Pranavathiyani G210 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 5 months ago by Devon Ryan86k • written 5 months ago by Pranavathiyani G210

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 5 months ago by cpad011210k
gravatar for Devon Ryan
5 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k 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 5 months ago by Devon Ryan86k
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