[BioC] combat error message

Peter Langfelder peter.langfelder at gmail.com
Fri May 16 16:41:34 CEST 2014


On Fri, May 16, 2014 at 3:48 AM, Natasha Sahgal <n.sahgal at qmul.ac.uk> wrote:
> Dear Peter,
>
> Thank you for your response.
>
> Yes, I should have seen it being confounding!
> Groups "a" and "b" are different, as I understand from my lab colleagues
> since they are 2 separate cell lines.
>
> Perhaps then I could compare gene lists to get an idea of possible 'a' and
> 'b' differences? Where I do the comparisons I want in group a, similarly
> in group b and then subsequently compare the 'a' gene list to the 'b' gene
> list.

Yes, this is a good idea. If you want to find genes that change
consistently in both cell lines, you could also do a meta-analysis
(i.e., calculate the p-value for your association of interest in "a"
and in "b", then combine them using a standard meta-analysis). An
alternative is to simply regress out the "a" vs. "b" indicator since
it seems to be perfectly orthogonal to the cont - 1- 2- 3- 4 variable,
but that assumes I understand your design correctly, which I may not.

Peter


>



More information about the Bioconductor mailing list