[BioC] HTqPCR problem

[David martin]

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


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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