[BioC] LIMMA, behaviour of 'lmFit': warnings

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Wed Mar 4 12:06:42 CET 2009


I am using the Limma package and I am getting warnings when trying to  
fit a linear model to my data in an "MAList", using a vector of  
weights (0 or 1) to discount genes that do not pass the low intensity  
filter in *all* my arrays.

I made a little example with made up data here that reproduces teh warnings:

# Make an MAList with 3 columns of 100 genes:
MA3$M<-matrix(rnorm(300), ncol=3)
MA3$A<-matrix(abs(rnorm(300)), ncol=3)

# create a weights vector, all 1 except for three elements turned to 0.
low3<-rep(1, times=100)
low3[c(10, 50, 90)]<-0

# no dye swap, straight replicates

# running the following command (no weights) works ok:
fit<-lmFit(MA3, design=design, weights=NULL) # ok

# if I try to use the weights, I get a warning:
fit<-lmFit(MA3, design=design, weights=low3) # warnings

Warning message:
In lmFit(MA3, design = design, weights = low3) :
   Some coefficients not estimable: coefficient interpretation may vary.

but the coefficients for the zero weighted elements are NA, however.

What is the reason for the warning? Shall I be concerned?

In my actual data about 25% of the genes are weighted zero.

This is my sessionInfo():

> sessionInfo()
R version 2.7.0 (2008-04-22)

LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United  
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices datasets  tcltk     utils     methods   base

other attached packages:
[1] limma_2.14.0   svSocket_0.9-5 svIO_0.9-5     R2HTML_1.59     
svMisc_0.9-5   svIDE_0.9-5

loaded via a namespace (and not attached):
[1] tools_2.7.0


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

More information about the Bioconductor mailing list