"controls" for genome-wide analysis

Question

[Bogdan]

Dear all,

'd like to have you suggestions please about the adequate "controls" when performing genome-wide analysis. For example, let's consider 1000 UP_REGULATED genes with increased PROTEIN X and HISTONE MARK Y (on the gene promoters or enhancers):

in order to show that PROTEIN X is related to HISTONE MARK Y for 1000 UP-regulated genes, what "controls" would you use for comparison :

-- 1000 RANDOM GENES

-- 1000 UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y

-- 1000 UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y

-- 1000 UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y

-- anything else ?

thanks a lot,

-- bogdan

[ATpoint]

Cross-posted:

https://support.bioconductor.org/p/128828/

https://bioinformatics.stackexchange.com/questions/11571/a-package-with-randomization-permutation-tests-for-genomic-analyses

I am not your judge but just saying: I find this disrespectful. You ask the members to invest effort in three separate communities while focusing information in a single thread should be the way to go here. This avoids double-effort and people might adjust their answers depending on other comments and answers. This is how a community typically works.

[Bogdan]

Thank you for your suggestions. I apologize if anyone felt uncomfortable : I was just willing to learn from everyone ;)

[ATpoint]

Yeah, this is exactly what you wrote on the last thread that was cross-posted to three different communities. Don't be surprised if you get no answers at all if you keep annoying people with this behaviour.

[Bogdan]

oh, well, sometime there is work pressure to get the work done ... My apologies, again ...

[zx8754]

Cross posting is fine if:

• there was no answer within 24 hours, and
• post contains the links to other posts.

On top of duplicating the effort from multiple users, asking the same Q on all sites within short period of time is "spamming".