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
Bioconductor
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.
Gordon
>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
>packages
>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
>give
>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()
>directly.
>
>Gordon
>
>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
>>
>>
>>--
>>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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