[BioC] reading imagene files with LIMMA

[Saroj Mohapatra]

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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