[R] confused about CORREP cor.LRtest

From: Mark W Kimpel <mwkimpel_at_gmail.com>
Date: Fri, 07 Mar 2008 12:29:07 -0500


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)

mwkimpel<at>gmail<dot>com

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Received on Fri 07 Mar 2008 - 17:31:22 GMT

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