[BioC] bug in limma?

[Gordon K Smyth]

Getting an error from a function when the input data is clearly wrong does
not constitute a bug in the software.

The latest versions of limma set the 'genes' component directly from the
gpr files.  This means that there is no longer any need to read the GAL
file with GenePix data.  I suggest that you stop using your GAL file which
for some reason does not match your gpr files.

Gordon

> 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