[BioC] reading imagene files with LIMMA

[Yi Xing]

Hello Saroj,

Thanks for your message. I think the problem is with the Field 
Dimensions. It looks like this for my file:

Field     Metarows Metacols Rows Cols
   Block1         1        1   15   14
   Block2         1        1   15   14
   Block3         1        1   15   14
   Block4         1        1   15   14
   Block5         1        1   15   14
   Block6         1        1   15   14
   Block7         1        1   15   14
   Block8         1        1   15   14
   Block9         1        1   15   14
   Block10        1        1   15   14
   Block11        1        1   15   14
   Block12        1        1   15   14
   Block13        1        1   15   14
   Block14        1        1   15   14
   Block15        1        1   15   14
   Block16        1        1   15   14
   Block17        1        1   15   14
   Block18        1        1   15   14
   Block19        1        1   15   14
   Block20        1        1   15   14
   Block21        1        1   15   14
   Block22        1        1   15   14
   Block23        1        1   15   14
   Block24        1        1   15   14
   Block25        1        1   15   14
   Block26        1        1   15   14
   Block27        1        1   15   14
   Block28        1        1   15   14
   Block29        1        1   15   14
   Block30        1        1   15   14
   Block31        1        1   15   14
   Block32        1        1   15   14

so read.imagene() calculates the total number of spots as prod(FD):

nspots <- prod(FD)
Y <- matrix(0, nspots, narrays)

  which is 2.046527e+74, causing the error in the next line.

Yi
On Jun 28, 2007, at 2:21 PM, Saroj Mohapatra wrote:

> Hello Yi,
>
> It is possible that there is a discrepancy between the number of spots 
> calculated from the Field Dimensions in header and the number of rows 
> it actually reads from the file.
>
> For example, in my Imagene 5.1 file:
> in the header, below "Begin Field Dimensions" I find the following:
> Metarows = 8
> Metacols = 4
> Rows = 15
> Cols = 12
>
> So, the total number of spots = 5760
> In the data section of my file, there are 5760 rows (excluding column 
> titles).
>
> Of course, the actual number would vary, you would have a different 
> number of spots. You could start with checking that the numbers match.
>
> Also, there should be something like "Begin Raw Data" before the first 
> line and "End Raw Data" after the last line of data section.
>
> Good luck!
>
> Saroj
>
> Yi Xing wrote:
>
>> Hi,
>>
>> I tried to read several Imagene files with LIMMA:
>>
>> library(limma)
>> targets<-readTargets()
>> files<-targets[,c("FileNameCy3","FileNameCy5")]
>> RG<-read.maimages(files,source='imagene')
>>
>> however, I got this error message:
>>
>> Read header information
>> Error in matrix(0, nspots, narrays) : matrix: invalid 'nrow' value 
>> (too large or NA)
>> In addition: Warning message:
>> NAs introduced by coercion
>>
>> What might be the problem and how to fix it? Thanks.
>>
>> Yi Xing
>>
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> <smohapat.vcf>