[BioC] Limma: Array weights question

[Sim, Fraser]

Hi,

I am trying to use arrayWeights on a design as follows:

>design = model.matrix(~-1+phenotype+SID)

Where SID refers to matched samples and phenotype as a cell phenotype
obtained from those samples.

I run array weights:

>arrayw <- arrayWeights(eset, design = design, trace = TRUE)
Coefficients not estimable: SIDC4 SIDP5 SIDSG7 
Error in chol.default(Zinfo) : 
  the leading minor of order 48 is not positive definite

What does this error mean?

Here is a summary of the samples. The phenotypes are labeled a through
k.

> colSums(design)
     a      b      c      d      e      f      g      h      i      j
k 
     3      4      4      4      4      5      5      5      5      5
5 
SID129 SID139  SID92  SIDC1  SIDC2  SIDC3  SIDC4  SIDP1  SIDP2  SIDP3
SIDP4 
     4      3      4      1      1      1      1      2      2      2
2 
 SIDP5 SIDSG3 SIDSG4 SIDSG5 SIDSG6 SIDSG7 
     2      4      4      4      4      4 


Thanks,
Fraser

> sessionInfo()
R version 2.8.1 (2008-12-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods

[8] base     

other attached packages:
[1] limma_2.16.4         RODBC_1.2-4          hgu133plus2cdf_2.3.0
[4] affy_1.20.2          Biobase_2.2.1        rcom_2.0-4          
[7] rscproxy_1.0-12     

loaded via a namespace (and not attached):
[1] affyio_1.10.1        preprocessCore_1.4.0