Re: [R] confused about CORREP cor.LRtest

From: dongxiaozhu <dongxiaozhu_at_yahoo.com>
Date: Thu, 13 Mar 2008 20:01:41 -0700 (PDT)

Hi Mark, sorry for the late response. I am now moving to my new job... When you use cor.balance() to estimate the correlation matrix, it is able to handle many variables (genes) at one time. What is returned should be a 497 by 497 correlation matrix. But when you use cor.LRtest() to calculate P-value, it can only work with a pair of genes at a time. Therefore, you need to put cor.LRtest() in a loop. For example.

PM <- matrix(NA, 497, 497)
for(i in 1:496)
for(j in (i+1):497)
PM[i,j] <- cor.LRtest() ## data involving only a pair genes

If you send me your data, I can write the exact code...

Best,

Dongxiao

Mark W Kimpel wrote:
>
> After some struggling with the data format, non-standard in
> BioConductor, I have gotten cor.balance in package CORREP to work. My
> desire was to obtain maximum-likelihood p-values from the same data
> object using cor.LRtest, but it appears that this function wants
> something different, which I can't figure out from the documentation.
>
> Briefly, my dataset consists of 36 samples from 12 conditions and I have
> 497 genes of interest to be correlated. The following works:
>
> M <- cor.balance(stddata, m = 3, G=497)
>
> The following does not:
> M.p <- cor.LRtest(stddata, m1 = 3, m2 = 3)
>
> Do I need to do something to stddata between example 1 and 2 or does "m"
> stand for something different in the two examples?
>
> sessionInfo follows. Thanks, Mark
>
> > sessionInfo()
> R version 2.7.0 Under development (unstable) (2008-03-05 r44683)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid tools stats graphics grDevices datasets utils
> [8] methods base
>
> other attached packages:
> [1] rat2302_2.0.1 Rgraphviz_1.17.13 graph_1.17.17
> [4] igraph_0.5 CORREP_1.5.0 e1071_1.5-17
> [7] class_7.2-41 affy_1.17.8 preprocessCore_1.1.5
> [10] affyio_1.7.13 Biobase_1.99.1
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.10
> --
>
> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN 46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 204-4202 Home (no voice mail please)
>
> mwkimpelgmailcom
>
> ______________________________________________
> R-help_at_r-project.org mailing list
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>

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