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

[J.delasHeras at ed.ac.uk]

Dear Gordon,

thanks for that, now I see what the warning was about. I was worried I  
may have misunderstood something.
As you say, it probably is best to change the warning when all coefs  
are NA for a given gene.

regards,

Jose

Quoting Gordon K Smyth <smyth at wehi.EDU.AU>:

> Dear Jose,
>
> 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.
>
> Best wishes
> Gordon
>
>> 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>
>>
>> Hi,
>>
>> 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<-new("MAList")
>> 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
>> design<-c(1,1,1)
>>
>> # 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)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
>> Kingdom.1252;LC_MONETARY=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
>>>
>>
>>
>> Jose
>>
>> -- 
>> 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
>> UK
>>
>> -- 
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.



-- 
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
UK

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