[BioC] problem with limma and BlueFuse

[M L Smith]

Hi,
There is an error with the limma code for using read.maimages with 
bluefuse.  I've informed the author (Gordon Smyth) and a fix will be 
included in the next release of limma.
In the meantime if you'd like my edited version of read.maimages 
that works with bluefuse data please email me and I'll send it to you.

Mike Smith

On 20 Jun 2006 at 17:51, Alessio Venier wrote:

> Hi,
> 
> I've a problem using limma with bluefuse output files (I've saved 
those files as .xls)
> I'm able to use one file per time without any trouble but when I try 
to load more than 
> one file using a "target" file, I receive an error message.
> I've installed R 2.3.1 and limma 2.7.3
> 
> Sample session below:
> 
> #Using right package!
> >library(limma)
> 
> #I create an object as a target from file
> > target<-
readTargets(file="targets.txt",path="C:\\Playground\\Micro")
> 
> #This is the object
> > target
>        SlideNumber Name   FileName     Cy3       Cy5
> array1           1   c1 array1.xls control treatment
> array2           2   c2 array2.xls control treatment
> 
> #and how I use the read.maimage
> > RG<-
read.maimages(target$FileName,source="bluefuse",path="C:\\Playg
round\\Micro")
> Read C:\Playground\Micro/array1.xls 
> Error in switch(source2, quantarray = { : could not find function 
"readBlueFuseHeader"
> 
> #I've also tried to use a vector with file names instead of a target 
object, 
> #but the result happen to be the same.
> 
> > files<-c("array1.xls","array2.xls")
> > RG<-
read.maimages(files,source="bluefuse",path="C:\\Playground\\Micro
")
> Read C:\Playground\Micro/array1.xls 
> Error in switch(source2, quantarray = { : could not find function 
"readBlueFuseHeader"
> 
> #I've not found any information about readBlueFuseHeader in the 
documentation (i'm using ver. 2.7.3)
> #If I call the function I receive the same error!
> 
> > readBlueFuseHeader()
> Error: could not find function "readBlueFuseHeader"
> 
> I'm a new user of R, please let me know what I'm doing wrong.
> 
> Kind Regards
> 
> Alessio
> 
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