Problem with gls.series in limma
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Fangxin Hong ▴ 810
@fangxin-hong-912
Last seen 10.2 years ago
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
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
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
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