Question: Gene Interaction Computation
0
gravatar for shaheryar
3.6 years ago by
shaheryar0
Korea, Republic Of
shaheryar0 wrote:

In GRN, every gene interacts with every other gene or sometimes with itself too and every gene connects with other genes with different concentration levels how we can measure those concentration levels I compute but it is giving a symmetric matrix means A -> B and B-> A same values but we know in reality A-> B and B->A have different values Can someone suggest how to compute these values?

Waiting Positive

ADD COMMENTlink modified 3.6 years ago by Robert Castelo2.3k • written 3.6 years ago by shaheryar0
Answer: Gene Interaction Computation
0
gravatar for Robert Castelo
3.6 years ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:

Hi,

it is difficult to figure out what your question is about. It seems related to how to calculate gene-gene associations from "concentration levels" measured for some kind of molecule that you do not specify (RNA?, metabolites?). If you are interested in software for estimating gene-gene associations from gene expression data I can recommend you to take a look at the qpgraph package at http://bioconductor.org/packages/qpgraph. Skimming through the vignettes can be a good starting point.

I also strongly recommend you to read thoroughly the posting guide at

http://www.bioconductor.org/help/support/posting-guide

if you plan to continue this discussion thread or post any new question on this support site.

cheers,

robert.

ADD COMMENTlink written 3.6 years ago by Robert Castelo2.3k

how to calculate associations from concentration levels of RNA. I am working on microarray data. Qgraph didnot solve my problem

ADD REPLYlink written 3.6 years ago by shaheryar0

what is your problem exactly? (what question are your trying to address, how does your input data looks like, etc.). PLEASE read the   posting guide.

ADD REPLYlink written 3.6 years ago by Robert Castelo2.3k
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