[BioC] ReadqPCR: [[hkgs,]] incorrect number of dimensions
Franklin Johnson [guest]
guest at bioconductor.org
Wed Mar 6 19:57:36 CET 2013
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.
In read.qPCR(qPCRBatch.lv) :
Incompatible phenoData object. Created a new one using sample name data derived from raw data.
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")
interest no interest
caseA 1 0
control 0 1
> ddCq.lv=deltaDeltaCq(qPCRBatch.lv, maxNACase=1, maxNAControl=1, hkgs=hkgs, contrastM=contM, case="interest", control="no interest", statCalc="arith", hkgCalc="arith")
Error in caseM[hkgs, ] : 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=deltaCq(qPCRBatch.lv, hkgs=hkgs, calc="arith")
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.
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 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):
 affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 tools_2.15.1 zlibbioc_1.4.0
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