[BioC] Error in calling read.maimages

[Wolfgang Huber]

Casper Shyr scripsit 30/03/11 06:30:
>
> Hello,
>    I encounter an error while reading in gpr files with read.maimages. My codes are:
>
> f<- function(x) as.numeric(x$Flags>  -50.5)
> RG<- read.maimages(targets, source="genepix", wt.fun=f)
>
> Error message is:
> Read GSM237424.gpr
> Read GSM237425.gpr
> Read GSM237426.gpr
> Read GSM237427.gpr
> Error in RG[[a]][, i]<- obj[, columns[[a]]] :
>    number of items to replace is not a multiple of replacement length
>
> I believe this is due to a different gpr format among some of the files. The first 4 that were read successfully are of "GenePix Result 3" type, and the next one which failed is of "GenePix Results 2" type. I checked the data, and found these versions differ in # of rows and columns.
>
> Does this mean I am unable to use Bioconductor to read + process gGenePix pr files that are of different output versions?

Dear Casper

no, but it means that you will have to write custom code, e.g., to read 
the different versions separately and then merge them together.

There is a reason why read.maimages does not automatically read and 
merge files from different arrays or from different versions of the 
image analysis software - namely, the data may not be directly 
comparable and applying the standard workflow would lead to undesirable 
"batch effects" and silly results. I am afraid you will need to put more 
effort into customising your approach to importing your data and working 
out an appropriate analysis approach.

	Hope this helps
	Wolfgang


>
> Thanks!
> Casper
>   		 	   		
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber