[BioC] LIMMA - "Subscript out of bounds" error

[Gordon K Smyth]

> Date: Mon, 9 May 2005 21:42:43 -0700 (PDT)
> From: Ankit Pal <pal_ankit2000 at yahoo.com>
> Subject: [BioC] LIMMA - "Subscript out of bounds" error
> To: bioconductor at stat.math.ethz.ch
>
> Hi All,
> I did a test run of Limma looking at the user's guide,

limma version number?

> on using the normalizeWithinArrays() function, I got a
> subscript out of bounds error. The steps I follwed
> were
>
>> files <- dir(pattern="*\\.gpr$")
>> RG <- read.maimages(files, source="genepix")
> Read result1.gpr
> Read result2.gpr
> Read result3.gpr
> Read result4.gpr
> Read result5.gpr
>> RG$genes <- readGAL()

This command (readGAL) is unnecessary and you should omit it.  It is only required with SPOT
files.  With GenePix, the gene IDs and annotation are already read from the gpr files.

>> RG$printer <- getLayout(RG$genes)
>> MA <- normalizeWithinArrays(RG)
> Error: subscript out of bounds

My guess is that the GAL file you have read doesn't match your gpr file, e.g., it has more rows
than the gpr files.  If this is the problem, it will go away if you stop using readGAL().

Gordon

> The gpr files I used were not modified and I did not
> filter out the bad spots.
> What could be the problem here and how do I solve it?
> Looking forward to a reply,
> -Ankit