[BioC] External expression data/ MAS5 Signal

[Laurent Gautier]

On Fri, Jun 14, 2002 at 02:08:24PM -0700, Peter Dimitrov wrote:
> Dear Laurant,
> 
> Thanks for the suggestion, it seems good place to plug MAS5. But before
> that, all of my data has to be transfered from Plobs to Cel.containers.
> What is the easiest way to convert Plob object to Cel.container? I've
> looked in the documentation, but still can't find an example of that, if
> there is any.

...if you did not subset your Plob objects, it should be technically possible... feel free to contribute a converter Plob->Cel.container...
(yep, it looks like there is no such converter in the package otherwise)

The other way is to load your data (again) through function like
'read.container.celfile' and do your data processing over these objects.

> 
> Regards,
> 
> Peter
> 
> P.S. There seems to be a bug in affy.subset(version 1.1.1).
> Specifically, the assigment of pData slot of the phenotypic object ph
> fails, because the subsetting operation of the data frame fails to
> return a data.frame(is this an R bug?):

'can't say, 'had no time to look at it...
(Rafael, Ben, Leslie, any idea ?)


> 
> ...
> ph <- phenoData(x)
> if (!is.null(pData(ph)) || length(chips) < nchips(x))
>     ph@pData <- pData(ph)[chips, ]
> ...
> 
> is.data.frame(pData(ph)[chips, ]) returns False and ph@pData is a data
> frame.
> 
> I choose to replace the asignment with this line:
> 
>     pData(ph) <- subset( pData(ph), rownames(pData(ph)) == chips )
> 
> assuming chips already is a list of chip names and not numeric indices.
> There are other solutions also.
> 
> 


Regards,



Laurent



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Laurent Gautier			CBS, Building 208, DTU
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