[BioC] weights in fitLM

[Street N.R.]

Hi

I recently upgraded to R 2.4.1 and ran biocLite to install the Bioconductor packages. This installs version 2.9.17 of limma. I also have my old version of R (2.1.1 which has version 2.3.3 of limma).

When I run

fit.O2<-lmFit(MA[isGene,], design.O2, weights=w)

in R 2.4.1 I get the error message 

Error in asMatrixWeights(weights, dim(M)) : 
        weights is of unexpected shape

but this works fine in R 2.1.1

This is how I made my weights matrix:

w<-modifyWeights(RG$weights,RG$genes$status,values=c("Cy3_oligo","Cy5_oligo"), multipliers=0)

excluded.spots<-spottypes[,1][spottypes[,1]!="cDNA"]
w<-modifyWeights(RG$weights,RG$genes$status,values=excluded.spots, multipliers=0)
# and then set anything with a weight of 0.1 to a value of 0
w[,][w[,]=="0.1"]<-0
 
the last four lines are using information from the spot types file.

Can anyone tell me why this is happening? I really need the spot weights to be used.

Thanks

Nat Street
---
Nathaniel Street
         University of Southampton
         Plants and Environment Lab
      School of Biological Sciences
   Basset Crescent East
   Southampton
 SO16 7PX
       tel: +44 (0) 2380 594268
  fax: +44 (0) 2380 594269
 n.r.street at soton.ac.uk

    http://www.populus.biol.soton.ac.uk/~nat 
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