[BioC] HTqPCR problem

[Heidi Dvinge]

> Is it possible from repeat row names in X?

It could be something along those lines, although duplicated row names in
X show throw an error already when creating the qPCRset object. In the
later versions, HTqPCR has been modified to inherit from eSet classes, and
be more strict about formats.

David, ould you please provide some more information about X and cat, or a
reproducible example? For me, the following works:

> X <- matrix(0, ncol=4, nrow=4)
> cat	<- matrix("OK", nrow=4, ncol=4)
> out <- new("qPCRset", exprs=X, flag=as.data.frame(X), featureCategory=cat)
> out
An object of class "qPCRset"
Size:  0 features, 4 samples
Feature types:
Feature names:		 NA NA NA ...
Feature classes:
Feature categories:	 OK, OK, OK, OK
Sample names:			 1 2 3 ...

Also, it looks like the object is created alright, but it's the 'show'
method that's not working. More specifically, the feature categories. Does
the following work?

featureCategory(out)

And if not, what happens if you say

out <- new("qPCRset", exprs=X, flag=as.data.frame(X),
featureCategory=as.matrix(cat))
out

Best,
\Heidi

> On Jun 20, 2012 6:36 AM, "David martin" <vilanew at gmail.com> wrote:
>
>> I'm manually building a qPCRset object that used to work until i switch
>> from R 2.12 to 2.15.
>>
>>
>> >dim(X) #data matrix (for the moment it contains only zero values)
>> [1] 3 72
>>
>> >dim(cat)#data matrix with charactacter string("OK")
>> [1] 3 72
>>
>> #Build Qpcr Object
>> out <- new("qPCRset", exprs=X, flag=as.data.frame(X),
>> featureCategory=cat)
>>
>>
>> > out
>> An object of class "qPCRset"
>> Size:  0 features, 72 samples
>> Feature types:
>> Feature names:           NA NA NA ...
>> Feature classes:
>> Error in `row.names<-.data.frame`(`***tmp*`, value = value) :
>>  invalid 'row.names' length
>> >
>>
>> What is the problem ????
>>
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