Question: ReadqPCR: [[hkgs,]] incorrect number of dimensions
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6.1 years ago by
Guest User12k
Guest User12k wrote:
Dear James, Thanks for your time and help with ReadqPCR and NormqPCR. I have worked a bit more with this NormqPCR; Very useful package, especially, for normalizing raw Ct data, determining housekeeping genes, etc. Thus far, I have been successful in working through the vignette. Although, I have one last inquiry. In order to confirm where the error is coming from, I have deduced my input file containing the raw Cq values to 2 conditions, 8 detectors, one technical replication. > qPCRBatch=read.qPCRqPCRBatch.lv) Warning message: In read.qPCRqPCRBatch.lv) : Incompatible phenoData object. Created a new one using sample name data derived from raw data. > exprs(qPCRBatch) caseA control actin 20.89 20.91 lox22 21.36 20.50 lox23 20.93 21.00 lox34 20.89 20.80 lox61 19.50 19.50 lox62 21.00 25.00 lox69 19.30 15.00 lox99 21.10 28.00 > contM=cbind(c(1,0), c(0,1)) > colnames(contM)=c("interest", "no interest") > rownames(contM)=sampleNamesqPCRBatch.lv) > contM interest no interest caseA 1 0 control 0 1 > hkgs="actin" > ddCq.lv=deltaDeltaCqqPCRBatch.lv, maxNACase=1, maxNAControl=1, hkgs=hkgs, contrastM=contM, case="interest", control="no interest", statCalc="arith", hkgCalc="arith") Error in caseM[hkgs[1], ] : incorrect number of dimensions Apart from the vignette, I didn't think I would need to identify hkgs in each sample?? What is odd is that I can complete the deltaCq function, > qPCRBatch.dcq=deltaCqqPCRBatch.lv, hkgs=hkgs, calc="arith") > exprs(qPCRBatch.dcq) caseA control actin 0.00 0.00 lox22 0.47 -0.41 lox23 0.04 0.09 lox34 0.00 -0.11 lox61 -1.39 -1.41 lox62 0.11 4.09 lox69 -1.59 -5.91 lox99 0.21 7.09 , but not the deltaDeltaCq function. This says to me that there is something wrong with my "case" vs. "control" comparison in the contrast matrix? However, like the vignette, I have my hkgs genes in both samples, as required by the same detectors for all samples requisite(which makes sense). Anyhow, it's been great to work with NormqPCR. Hopefully, I can complete it by getting the deltaDeltaCq output. If you have a chance, can you please take a look at the scripts and correct me where I'm wrong. Respectfully, Franklin -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.14.0 NormqPCR_1.4.0 RColorBrewer_1.0-5 ReadqPCR_1.4.0 affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 tools_2.15.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
readqpcr normqpcr • 2.0k views
ADD COMMENTlink modified 6.1 years ago by James Perkins120 • written 6.1 years ago by Guest User12k
Answer: ReadqPCR: [[hkgs,]] incorrect number of dimensions
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gravatar for James Perkins
6.1 years ago by
James Perkins120
James Perkins120 wrote:
Hi Franklin, It looks like the problem is due to you only having 1 replicate for case and 1 for control, and so it can't work out stats etc. I will work on a fix for this, in the meantime you can work out delta delta Cq by subracting 1 column from qPCRBatch.dcq from the other (followed by 2^ tranformation). Cheers, hope that helps, Jim On 6 March 2013 19:57, Franklin Johnson [guest] <guest@bioconductor.org>wrote: > > Dear James, > > Thanks for your time and help with ReadqPCR and NormqPCR. > > I have worked a bit more with this NormqPCR; > Very useful package, especially, for normalizing raw Ct data, determining > housekeeping genes, etc. > > Thus far, I have been successful in working through the vignette. > Although, I have one last inquiry. > In order to confirm where the error is coming from, I have deduced my > input file containing the raw Cq values to 2 conditions, 8 detectors, one > technical replication. > > > qPCRBatch=read.qPCRqPCRBatch.lv) > Warning message: > In read.qPCRqPCRBatch.lv) : > Incompatible phenoData object. Created a new one using sample name data > derived from raw data. > > > exprs(qPCRBatch) > caseA control > actin 20.89 20.91 > lox22 21.36 20.50 > lox23 20.93 21.00 > lox34 20.89 20.80 > lox61 19.50 19.50 > lox62 21.00 25.00 > lox69 19.30 15.00 > lox99 21.10 28.00 > > > contM=cbind(c(1,0), c(0,1)) > > colnames(contM)=c("interest", "no interest") > > rownames(contM)=sampleNamesqPCRBatch.lv) > > contM > interest no interest > caseA 1 0 > control 0 1 > > > hkgs="actin" > > ddCq.lv=deltaDeltaCqqPCRBatch.lv, maxNACase=1, maxNAControl=1, > hkgs=hkgs, contrastM=contM, case="interest", control="no interest", > statCalc="arith", hkgCalc="arith") > Error in caseM[hkgs[1], ] : incorrect number of dimensions > > Apart from the vignette, I didn't think I would need to identify hkgs in > each sample?? > > What is odd is that I can complete the deltaCq function, > > qPCRBatch.dcq=deltaCqqPCRBatch.lv, hkgs=hkgs, calc="arith") > > exprs(qPCRBatch.dcq) > caseA control > actin 0.00 0.00 > lox22 0.47 -0.41 > lox23 0.04 0.09 > lox34 0.00 -0.11 > lox61 -1.39 -1.41 > lox62 0.11 4.09 > lox69 -1.59 -5.91 > lox99 0.21 7.09 > > , but not the deltaDeltaCq function. > This says to me that there is something wrong with my "case" vs. "control" > comparison in the contrast matrix? However, like the vignette, I have my > hkgs genes in both samples, as required by the same detectors for all > samples requisite(which makes sense). > > Anyhow, it's been great to work with NormqPCR. > Hopefully, I can complete it by getting the deltaDeltaCq output. > > If you have a chance, can you please take a look at the scripts and > correct me where I'm wrong. > > Respectfully, > Franklin > > > > > -- output of sessionInfo(): > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] limma_3.14.0 NormqPCR_1.4.0 RColorBrewer_1.0-5 > ReadqPCR_1.4.0 affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 > tools_2.15.1 zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Dr James R Perkins Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Street London, WC1E 6BT UK email: j.perkins@ucl.ac.uk [[alternative HTML version deleted]]
ADD COMMENTlink written 6.1 years ago by James Perkins120
Dear James, Now I can recognize the meaning of: Error in caseM[hkgs[1], ] : incorrect number of dimensions. Given your correction, I can now calculate delta delta Cq too. Also, I have a better understanding of how NormqPCR operates and can generate transformed values. Thanks for everything. If I have questions down the road with another, larger dataset, I hope you don't mind if I contact you again. Respectfully, Franklin Johnson ________________________________ From: jimrperkins@gmail.com [jimrperkins@gmail.com] on behalf of James Perkins [j.perkins@ucl.ac.uk] Sent: Wednesday, March 06, 2013 11:53 PM To: Franklin Johnson [guest] Cc: Bioconductor@r-project.org; FRANKLIN.JOHNSON@wsu.edu Subject: Re: [BioC] ReadqPCR: [[hkgs,]] incorrect number of dimensions Hi Franklin, It looks like the problem is due to you only having 1 replicate for case and 1 for control, and so it can't work out stats etc. I will work on a fix for this, in the meantime you can work out delta delta Cq by subracting 1 column from qPCRBatch.dcq from the other (followed by 2^ tranformation). Cheers, hope that helps, Jim On 6 March 2013 19:57, Franklin Johnson [guest] <guest@bioconductor.org<mailto:guest@bioconductor.org>> wrote: Dear James, Thanks for your time and help with ReadqPCR and NormqPCR. I have worked a bit more with this NormqPCR; Very useful package, especially, for normalizing raw Ct data, determining housekeeping genes, etc. Thus far, I have been successful in working through the vignette. Although, I have one last inquiry. In order to confirm where the error is coming from, I have deduced my input file containing the raw Cq values to 2 conditions, 8 detectors, one technical replication. > qPCRBatch=read.qPCRqPCRBatch.lv) Warning message: In read.qPCRqPCRBatch.lv) : Incompatible phenoData object. Created a new one using sample name data derived from raw data. > exprs(qPCRBatch) caseA control actin 20.89 20.91 lox22 21.36 20.50 lox23 20.93 21.00 lox34 20.89 20.80 lox61 19.50 19.50 lox62 21.00 25.00 lox69 19.30 15.00 lox99 21.10 28.00 > contM=cbind(c(1,0), c(0,1)) > colnames(contM)=c("interest", "no interest") > rownames(contM)=sampleNamesqPCRBatch.lv) > contM interest no interest caseA 1 0 control 0 1 > hkgs="actin" > ddCq.lv=deltaDeltaCqqPCRBatch.lv, maxNACase=1, maxNAControl=1, hkgs=hkgs, contrastM=contM, case="interest", control="no interest", statCalc="arith", hkgCalc="arith") Error in caseM[hkgs[1], ] : incorrect number of dimensions Apart from the vignette, I didn't think I would need to identify hkgs in each sample?? What is odd is that I can complete the deltaCq function, > qPCRBatch.dcq=deltaCqqPCRBatch.lv, hkgs=hkgs, calc="arith") > exprs(qPCRBatch.dcq) caseA control actin 0.00 0.00 lox22 0.47 -0.41 lox23 0.04 0.09 lox34 0.00 -0.11 lox61 -1.39 -1.41 lox62 0.11 4.09 lox69 -1.59 -5.91 lox99 0.21 7.09 , but not the deltaDeltaCq function. This says to me that there is something wrong with my "case" vs. "control" comparison in the contrast matrix? However, like the vignette, I have my hkgs genes in both samples, as required by the same detectors for all samples requisite(which makes sense). Anyhow, it's been great to work with NormqPCR. Hopefully, I can complete it by getting the deltaDeltaCq output. If you have a chance, can you please take a look at the scripts and correct me where I'm wrong. Respectfully, Franklin -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.14.0 NormqPCR_1.4.0 RColorBrewer_1.0-5 ReadqPCR_1.4.0 affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 tools_2.15.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr James R Perkins Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Street London, WC1E 6BT UK email: j.perkins@ucl.ac.uk<mailto:j.perkins@ucl.ac.uk> [[alternative HTML version deleted]]
ADD REPLYlink written 6.1 years ago by Johnson, Franklin Theodore140
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