[BioC] limma package : Error in sigToEnv(signature,fdef) : Tr ying to get slot "signature" from an object of a basic class ("NULL") wi t h no slots

[He, Yiwen (NIH/CIT)]

FYI:

I did a trackback() and saw that the coefficients, sigmas, and other
statistics were all produced before the sigToEnv() function caused the
problem. I started a new R session, loaded the package and tried it again --
and it worked properly! I was using an older version of limma, detached it
and installed/loaded the new version in the same session -- might be the
problem.

Thank you for your help!

Yiwen

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Wednesday, April 06, 2005 4:43 PM
To: He, Yiwen (NIH/CIT)
Cc: 'bioconductor at stat.math.ethz.ch'
Subject: Re: [BioC] limma package : Error in sigToEnv(signature,fdef) : Tr
ying to get slot "signature" from an object of a basic class ("NULL") wit h
no slots

He, Yiwen (NIH/CIT) wrote:
> Thanks James, but I did do data <- as.matrix(data) before running lmFit,
and
> is.matrix(data) returns TRUE. ("data" is just for illustration purpose,
but
> thanks for pointing out the variable name issue.) 
> 
> Any other suggestions?

You could always call traceback() after the error to see where things 
went wrong. The problem may be obvious at that point, or it may give you 
an idea what function to step through using debug().

An error such as yours indicates to me that lmFit() thinks you are 
passing some sort of an S4 object and is trying to get the contents of a 
slot. I don't see how this is possible with a numeric matrix (and I 
can't reproduce it here). Can you give a toy example that anybody could 
run that causes the error?


> 
> Yiwen
> 

-- 
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