[R] Help in error : SAM function in library siggenes

[James MacDonald]

siggenes is part of Bioconductor, and the author is Holger Schwender.
You should ask Holger first (holger.schw at gmx.de), and the BioC list
second.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Duncan Murdoch <dmurdoch at pair.com> 01/29/04 06:54AM >>>
On Thu, 29 Jan 2004 01:03:56 -0800 (PST), you wrote:

>Hi,
>
>I had the following situation and I greatly appreciate
>any advice.
>
>SAM gave the following error  :
>
>"Error in var(v) : missing observations in cov/cor"
>
>when applied on a dataset. The error was traced to a
>variance computation of a vector containing NA in
>fudge() [a subroutine called by SAM()]. This vector is
>a computational output in fudge() :
>
>"cv[i] <- sqrt(var(v))/mean(v)"
>
>The same error was encountered when SAM was applied to
>other similar datasets. Would modifying the statement
>to "var(v, na.rm=TRUE)" be a possibility?

SAM() and sam() are different names in R, but neither of them is in
the base packages.  Which package did you find sam() in?  You probably
want to ask the author of the package if this modification would be
safe.

Duncan Murdoch

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