[BioC] bug in limma?

[Simon Melov]

Hi,
this may be my ignorance, but I am persistently getting an error upon 
reading in one data set. It seems to be in the implementation of the 
gene list in the normalized MA.

The error I am getting after trying to fit is..

 > fit <- lmFit(MA, design)
Error: (subscript) logical subscript too long

After checking the size of M,A, and the gene list in MA, its clear that 
M and A are the correct size. But for some reason, the genelist is 
incorrectly sized however you look at it (which is not the case in the 
input gpr files..)

show(MA)
An object of class "MAList"
$genes
   Block Row Column                    ID                  Name
1     1   1      1           Human Cot 1           Human Cot 1
2     1   1      2 Spot Report Product 2 Spot Report Product 2
3     1   1      3        B-Human Actin         B-Human Actin
4     1   1      4                Buffer                Buffer
5     1   1      5                Poly A                Poly A
16891 more rows ...

 > MA$M[16891:16896,]
          MB12A04     MB12A05  ect..
[1,] -0.08841763 -0.24117406
[2,] -0.01282521 -0.09876827
[3,]  0.16414844  0.44696644
[4,]  0.26038965  0.51199616
[5,]  0.28553731 -0.51235751
[6,]  0.03343551  0.31066801

 > MA$M[16894:16897,]
Error: subscript out of bounds

This is fine, as there are only 16896 rows.

But for the MA$genes..

MA$gen[16894:16897,]
       Block Row Column                    ID                  Name
16894    32  22     22 Spot Report Product 8 Spot Report Product 8
16895    32  22     23                Buffer                Buffer
16896    32  22     24                Buffer                Buffer
NA       NA  NA     NA                  <NA>                  <NA>

  MA$gen[16894:16898,]
       Block Row Column                    ID                  Name
16894    32  22     22 Spot Report Product 8 Spot Report Product 8
16895    32  22     23                Buffer                Buffer
16896    32  22     24                Buffer                Buffer
NA       NA  NA     NA                  <NA>                  <NA>
NA.1     NA  NA     NA                  <NA>                  <NA>

MA$gen[16894:16899,]
       Block Row Column                    ID                  Name
16894    32  22     22 Spot Report Product 8 Spot Report Product 8
16895    32  22     23                Buffer                Buffer
16896    32  22     24                Buffer                Buffer
NA       NA  NA     NA                  <NA>                  <NA>
NA.1     NA  NA     NA                  <NA>                  <NA>
NA.2     NA  NA     NA                  <NA>                  <NA>

and so on.

Is this why I'm getting the fit error listed above, ie is this a bug?

Simon 
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