Fwd: Re: [BioC] Problem with gls.series in limma

Gordon Smyth smyth at wehi.edu.au
Thu Sep 23 03:19:18 CEST 2004

Actually on checking back through the records, I can see that none of the 
release versions of limma would have given the below error. You must be 
using an
in-between version of limma from between Feb 8 and March 20 of this year
with a later version (after March 20) of statmod.

As an Bioinformatics Specialist, I'm sure you will appreciate that it is a 
good idea
to quote the version number of software that you're asking questions about, 
and that
it is a good idea to try updating to current software to see if it solves 
your problem.


>Date: Thu, 23 Sep 2004 10:55:07 +1000
>To: fhong at salk.edu
>From: Gordon Smyth <smyth at wehi.edu.au>
>Subject: Re: [BioC] Problem with gls.series in limma
>Cc: bioconductor at stat.math.ethz.ch
>You're using an older version of limma with a newer version of statmod. 
>This may have
>occured because you have the last Bioconductor release of limma with a 
>more recent
>version of statmod from CRAN. The problem is that Bioconductor updates its 
>only once every 6 months (unless you use the developmental version, which 
>I don't
>recommend) while CRAN packages are updated as required.
>The solution is to update limma and statmod directly from CRAN, which will 
>you the current versions of both packages. Just use
>  install.packages("limma")
>or use the drop down menu if you're using Windows.
>BTW, I recommend that you move to mFit() rather than using gls.series() 
>At 09:52 AM 23/09/2004, Fangxin Hong wrote:
>>Hi there;
>>    I tried to use gls.series to get least square fit for each gene, but I
>>got the following error message:
>>Loading required package: statmod
>>Attaching package 'statmod':
>>         The following object(s) are masked from package:limma :
>>          matvec vecmat
>>Error in randomizedBlockFit(y, X, Z, fixed.estimates = FALSE) :
>>         unused argument(s) (fixed.estimates ...)
>>Any clue?
>>Thanks a lot!
>>Fangxin Hong, Ph.D.
>>Bioinformatics Specialist
>>Plant Biology Laboratory
>>The Salk Institute
>>10010 N. Torrey Pines Rd.
>>La Jolla, CA 92037
>>E-mail: fhong at salk.edu

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