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@med.umich.edu] Sent: Wednesday, April 06, 2005 2:51 PM To: He, Yiwen (NIH/CIT) Cc: 'bioconductor@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

"He, Yiwen (NIH/CIT)" <heyiwen@mail.nih.gov> writes: > 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 might try calling traceback() right after the error occurs and post the output. That may be informative as to the root cause of the error. + seth

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