Entering edit mode
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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