[BioC] limma question

[Sun, Yezhou]

Hello, Jim,

Thank you very much for all the suggestions. The problem was solved.
However I got several new questions:

1. what is the exact meaning of -1, 0, 1 in design matrix?

2. I also ran SAM on this data set. There is almost no overlapping
between top genes picked up by SAM and limma. What could this imply?

3. It seems that lmFit requires the number of columns in data set be
same as the number of arrays in design matrix. So there is no way to put
probe ID into data set. There are numbers listed in ProbeID field in
output from topTable(). Are these numbers supposed to be row ID in data
set?

My data set is from GE Codelink platform and has been median centered
and log2 transformed.

Thanks a lot.

Yezhou

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Friday, February 24, 2006 5:31 PM
To: Sun, Yezhou
Cc: BioConductor_list; Zhang, Weijia
Subject: Re: [BioC] limma question

Sun, Yezhou wrote:
> Hi, Jim,
> 
> I tried what you suggested but it's still not working. Got same error
> message:
> 
> 
>>fit<-lmFit(d[, -1], design)
> 
> Error in qr(x) : NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning message:
> NAs introduced by coercion 
> 
> 
> I think the problem is still in data frame but I don't know what it
is.
> The user guide has no detailed description for single channel data
set. 

Affy data are single channel, and I think there are two or three 
examples in the user guide.

lmFit() is expecting some sort of BioC type object (exprSet, MAlist, 
marrayNorm, PLMset) or a numeric matrix. A matrix can only contain data 
of one type (character, factor, numeric, etc), whereas a data.frame can 
contain data of mixed types. One of the first things lmFit() is doing to

your data.frame is coercing to a matrix, which I think is the reason for

the Warning message saying NAs introduced by coercion. I figured that 
the first column was the problem, but you need to see if there are any 
other NAs in the data.frame, or better yet do

new.d <- as.matrix(d[,-1])

and look for the NAs.

Best,

Jim


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



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