Can I adjust family relationship in Limma?
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@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia
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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
Microarray graph limma Microarray graph limma • 779 views
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