[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)]

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?

Yiwen

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Wednesday, April 06, 2005 2:51 PM
To: He, Yiwen (NIH/CIT)
Cc: 'bioconductor at stat.math.ethz.ch'
Subject: Re: [BioC] limma package : Error in sigToEnv(signature, fdef) :
Trying to ge t slot "signature" from an object of a basic class ("NULL")
with no slots

He, Yiwen (NIH/CIT) wrote:
> Hi, I was using an older (11/23/04) version of limma package and it worked
> fine for my log ratio data. I just installed the latest version (2/24/05)
> but got this error message when I did:
> 
>  
> 
> 
>>lmFit(data)                  # data is just a matrix of log ratios.
> 
> 
>  
> 
> Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from
an
> object of a basic class ("NULL") with no slots

My bet is that data (bad variable name, btw; you are masking an existing 
R function) is not a matrix, but a data.frame. Try

lmFit(as.matrix(data))

HTH,

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