[BioC] HTqPCR problem

[Heidi Dvinge]

Hi David,

> No X lmatrix is empty.
>
> Here is a snippet to reproduce the problem. test on your side and see if
> you get the same error
>
> library(HTqPCR)
> X <- matrix(0,3,72)
> cat <- data.frame(matrix("OK", ncol=72, nrow=3), stringsAsFactors=FALSE)
> out <- new("qPCRset", exprs=X, flag=as.data.frame(X), featureCategory=cat)
> out
>
Thanks for the example, I get the same output now. Turns out the problem
is due to missing featureNames, since this can't be taken from the
rownames of your X as is expected by qPCRsets per default. For example:

> X <- matrix(0,3,72)
> cat <- data.frame(matrix("OK", ncol=72, nrow=3))
> 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
> head(featureNames(out))
character(0)
> featureNames(out) <- paste("ft", 1:nrow(out), sep="")
> out
An object of class "qPCRset"
Size:  3 features, 72 samples
Feature types:
Feature names:		 ft1 ft2 ft3 ...
Feature classes:
Feature categories:	 OK
Sample names:			 1 2 3 ...

I'll add a more informative error message. In the meantime, if you convert
'cat' to a matrix, it seems to work fine (at least this part):

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


HTH
\Heidi

>
> ANy idea why this not working ?
>  > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      splines   stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>   [1] HH_2.3-15           latticeExtra_0.6-19 leaps_2.9
>   [4] lattice_0.20-6      gplots_2.10.1       KernSmooth_2.23-7
>   [7] caTools_1.13        bitops_1.0-4.1      gdata_2.8.2
> [10] gtools_2.6.2        multcomp_1.2-12     survival_2.36-14
> [13] mvtnorm_0.9-9992    pROC_1.5.1          plyr_1.7.1
> [16] HTqPCR_1.10.0       limma_3.12.0        RColorBrewer_1.0-5
> [19] Biobase_2.16.0      BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] affy_1.34.0           affyio_1.24.0         BiocInstaller_1.4.6
> [4] preprocessCore_1.18.0 stats4_2.15.0         tools_2.15.0
> [7] zlibbioc_1.2.0
>  >
>
>
>
>
> On 06/20/2012 01:44 PM, wenhuo hu wrote:
>> Is it possible from repeat row names in X?
>> 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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