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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
--
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