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@salk.edu >From: Gordon Smyth <smyth@wehi.edu.au> >Subject: Re: [BioC] Problem with gls.series in limma >Cc: bioconductor@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@salk.edu