HTqPCR problem
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David ▴ 860
@david-3335
Last seen 3.8 years ago
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 ????
qPCR qPCR • 1.2k views
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wenhuo hu ▴ 200
@wenhuo-hu-5208
Last seen 3.6 years ago
United States
Is it possible from repeat row names in X? On Jun 20, 2012 6:36 AM, "David martin" <vilanew@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 ???? > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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> 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 ???? >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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 ???? >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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 ???? >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Perfect , works !!! On 06/20/2012 03:06 PM, Heidi Dvinge wrote: > out<- new("qPCRset", exprs=X, flag=as.data.frame(X), > featureCategory=as.matrix(cat))
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