[BioC] Can I adjust family relationship in Limma?

[Gordon K Smyth]

Dear Jack,

No, not exactly.  If I understand you correctly, what you are asking for 
is an open research question, and is not offered by any current software 
package.

Note that a kinship correlation matrix does not translate into a 
correlation matrix for an analysis of microarray expression data from the 
same samples.  The within-family correlations of expression values will 
generally be quite a bit smaller than your kinship graph would have 
suggested.

However you can do an approximate analysis in limma.  If you can separate 
the samples into family groups, then you can set family to be a blocking 
variable in limma (using the block argument of the duplicateCorrelation 
and lmFit functions).  limma will then estimate a within-family 
correlation from the expression data and will use it for the differential 
expression analysis.  This will be of a simple nature, with one 
correlation value used for all families and all genes.  Nevertheless, much 
better than nothing.

Best wishes
Gordon

> Date: Tue, 14 Aug 2012 15:14:15 -0400
> From: Yao Chen <chenyao.bioinfor at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] [Limma] Can I adjust family relationship in Limma?
>
> Hi all,
>
> I have thousands samples from different families. Now I want to find
> differential expressed gene using Limma. I have family correlation matrix
> from kinship, Is there any way I can include these correlation in lmFit?
>
> Thanks,
> Jack

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