[BioC] bug in limma?

[James Wettenhall]

Simon,

It would be helpful to know which version of limma you are 
using and how you read in your genelist.  Did you use
RG$genes <- readGAL()  ?

Do you have any blank lines at the end of your GAL file?

Have a look at the help for readGAL and read.table (which 
readGAL calls).

What happens if you subset your genes component of MA (or RG), 
then does lmFit work?

i.e.

MA$genes <- MA$genes[1:16896,]

Regards,
James

On Thu, 29 Jan 2004, Simon Melov wrote:

> 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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James Wettenhall                                  Tel: (+61 3) 9345 2629
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