[R] co-expression network of coding-noncoding genes

Bert Gunter bgunter.4567 at gmail.com
Wed Jan 11 23:38:10 CET 2017

Wrong list.

Post on the Bioconductor list.

-- Bert

On Jan 11, 2017 5:15 PM, "Elham - via R-help" <r-help at r-project.org> wrote:

hello all,

I have 9 experiments (human RNAseq data (control/treatment)),I did RNAseq
analysis by CLC genomics,after normalization I calculated correlation, I
have many pairs of coding and lncoding molecules that correlate according
to their expression,I filtered them (> 0.9 and < -0.9). Additionally, I've
considered the pairs that have p-values < 0.001,but they are many pairs yet.

now for more filtering I want to consider the pairs of coding-non coding,
which are both deferentially expressed.
how can I have DE for all treated vs all controls samples for coding and DE
for all treated vs all controls samples for noncoding?

I should say that each experiment is effect of one drug on one cancer
(drugs and cancers are different in each experiment ) but the platform is
similar and all of them are Illumina HiSeq 2000 (Homo sapiens)

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