[BioC] LIMMA, behaviour of 'lmFit': warnings
Gordon K Smyth
smyth at wehi.EDU.AU
Thu Mar 5 23:09:54 CET 2009
The warning from lmFit was introduced a while ago (a year or so) as a
result of a user request on this mailing list.
The warning is to remind people that, when some of the coefs for a
particular probe become NA but others are estimable, the interpretation of
the remaining coefs is changed for that probe. This is an unavoidable
characteristic of missing values.
I agree the warning doesn't make sense when the coefs are either all NA or
all estimable, as in your example below. I'll fix that.
> Date: Wed, 04 Mar 2009 11:06:42 +0000
> From: J.delasHeras at ed.ac.uk
> Subject: [BioC] LIMMA, behaviour of 'lmFit': warnings
> To: Bioconductor mailing list <bioconductor at stat.math.ethz.ch>
> 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():
> 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:
>  stats graphics grDevices datasets tcltk utils methods base
> other attached packages:
>  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):
>  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.
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