Hi Franklin

Thanks for pointing out about the plate ID sample label problem - in fact,
that should read "plate" only, not plate ID - I will update the vignette
appropriately.

A couple of issues with your file:

1 your plate ids are more sample descriptions - it is expected that each
plate should have the same number of wells.

Your detectors are indeed different for the different samples - you have
added TechRep.1 to the end of the detectors in sample one, and TechRep.2 to
those in sample two.

The TechReps.N (notice the s - I will change the text in the vignette to
make it clear) is added when the file contains 2 or more identical
detectors for the same sample - i.e. the sample can be thought of as a
separate biological sample, then within the sample you have a number of
technical replicates, i.e. the same sample, and detector but a different Cq
value. Thus it is necessary to append TechReps.N to the end to distinguish
between tech reps. This was introduced originally to deal with sds files
where the same sample could have more than one identically named detector.

Hope that helps - basically if you take the .1 or .2 off the end of the
feature names, the file should be readable.

Cheers,

Jim


On 24 February 2013 23:50, Franklin Johnson [guest]
<guest@bioconductor.org>wrote:

>
> Dear James and Matthias,
>
> I am trying to repeat the steps to read in data.
> The data is modified from my experiment into a tab-delim file which is
> identical to qPCR.techReps.txt:
> Well    Plate ID        Sample  Detector        Cq
> 1       caseA   one     actin_untreated_0d_TechRep.1    20.3
> 2       caseB   one     actin_triton_1d_TechRep.1       20.91
> 3       caseB   one     actin_triton_3d_TechRep.1       21.08
> 4       caseB   one     actin_triton_7d_TechRep.1       21
> 5       caseB   one     actin_triton_14d_TechRep.1      21.32
> 6       caseC   one     actin_meja_1d_TechRep.1 21.36
> 7       caseC   one     actin_meja_3d_TechRep.1 21.22
> 8       caseC   one     actin_meja_7d_TechRep.1 21.79
> 9       caseC   one     actin_meja_14d_TechRep.1        22.07
> 1       caseA   two     actin_untreated_0d_TechRep.2    20.1
> 2       caseB   two     actin_triton_1d_TechRep.2       21.1
> 3       caseB   two     actin_triton_3d_TechRep.2       21.12
> 4       caseB   two     actin_triton_7d_TechRep.2       21.3
> 5       caseB   two     actin_triton_14d_TechRep.2      21.21
> 6       caseC   two     actin_meja_1d_TechRep.2 21.5
> 7       caseC   two     actin_meja_3d_TechRep.1 21.4
> 8       caseC   two     actin_meja_7d_TechRep.2 22
> 9       caseC   two     actin_meja_14d_TechRep.2        22.1
> 10      caseA   one     lox22_untreated_0d_TechRep.1    22.28
> 11      caseB   one     lox22_triton_1d_TechRep.1       23.65
> 12      caseB   one     lox22_triton_3d_TechRep.1       24.77
> 13      caseB   one     lox22_triton_7d_TechRep.1       23.99
> 14      caseB   one     lox22_triton_14_TechRep.1       24.47
> 15      caseC   one     lox22_meja_1d.TechRep.1 22.13
> 16      caseC   one     lox22_meja_3d_TechRep.1 21.99
> 17      caseC   one     lox22_meja_7d_TechRep.1 24.17
> 18      caseC   one     lox22_meja_14d_TechRep.1        24.17
> 10      caseA   two     lox22_untreated_0d_TechRep.2    22.4
> 11      caseB   two     lox22_triton_1d_TechRep.2       23.84
> 12      caseB   two     lox22_triton_3d_TechRep.2       24.9
> 13      caseB   two     lox22_triton_7d_TechRep.2       24.2
> 14      caseB   two     lox22_triton_14_TechRep.2       24.6
> 15      caseC   two     lox22_meja_1d.TechRep.2 22.2
> 16      caseC   two     lox22_meja_3d_TechRep.2 22.3
> 17      caseC   two     lox22_meja_7d_TechRep.2 24.3
> 18      caseC   two     lox22_meja_14d_TechRep.2        24.2
>
> The first error I received is:
> > qPCR.mine<-file.path(path, "refinedCtData2.txt")
> > qPCRBatch.qPCR=read.qPCR(qPCR.mine)
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>  :
>   line 1 did not have 6 elements
>
> I adjusted my file, but now I get this error:
> > qPCR.example<-file.path("refinedCtData.txt")
> > qPCRBatch.qPCR=read.qPCR(qPCR.example)
> Error in .read.qPCR(filename, verbose) :
>   File incorrect, make sure that detectors are the same for all samples
>
> However, from appearance of the file, the detectors are the same for all
> samples doesn't seem logical, nor intuitive. Although,
> I changed the detectors around:
>
> Well    Plate ID        Sample  Detector        Cq
> 1       caseA   one     actin_untreated_0d_TechRep.1    20.3
> 2       caseB   one     actin_triton_1d_TechRep.1       20.91
> 3       caseB   one     actin_triton_3d_TechRep.1       21.08
> 4       caseB   one     actin_triton_7d_TechRep.1       21
> 5       caseB   one     actin_triton_14d_TechRep.1      21.32
> 6       caseC   one     actin_meja_1d_TechRep.1 21.36
> 7       caseC   one     actin_meja_3d_TechRep.1 21.22
> 8       caseC   one     actin_meja_7d_TechRep.1 21.79
> 9       caseC   one     actin_meja_14d_TechRep.1        22.07
> 1       caseA   one     actin_untreated_0d_TechRep.2    20.1
> 2       caseB   one     actin_triton_1d_TechRep.2       21.1
> 3       caseB   one     actin_triton_3d_TechRep.2       21.12
> 4       caseB   one     actin_triton_7d_TechRep.2       21.3
> 5       caseB   one     actin_triton_14d_TechRep.2      21.21
> 6       caseC   one     actin_meja_1d_TechRep.2 21.5
> 7       caseC   one     actin_meja_3d_TechRep.1 21.4
> 8       caseC   one     actin_meja_7d_TechRep.2 22
> 9       caseC   one     actin_meja_14d_TechRep.2        22.1
> 10      caseA   two     lox22_untreated_0d_TechRep.1    22.28
> 11      caseB   two     lox22_triton_1d_TechRep.1       23.65
> 12      caseB   two     lox22_triton_3d_TechRep.1       24.77
> 13      caseB   two     lox22_triton_7d_TechRep.1       23.99
> 14      caseB   two     lox22_triton_14_TechRep.1       24.47
> 15      caseC   two     lox22_meja_1d.TechRep.1 22.13
> 16      caseC   two     lox22_meja_3d_TechRep.1 21.99
> 17      caseC   two     lox22_meja_7d_TechRep.1 24.17
> 18      caseC   two     lox22_meja_14d_TechRep.1        24.17
> 10      caseA   two     lox22_untreated_0d_TechRep.2    22.4
> 11      caseB   two     lox22_triton_1d_TechRep.2       23.84
> 12      caseB   two     lox22_triton_3d_TechRep.2       24.9
> 13      caseB   two     lox22_triton_7d_TechRep.2       24.2
> 14      caseB   two     lox22_triton_14_TechRep.2       24.6
> 15      caseC   two     lox22_meja_1d.TechRep.2 22.2
> 16      caseC   two     lox22_meja_3d_TechRep.2 22.3
> 17      caseC   two     lox22_meja_7d_TechRep.2 24.3
> 18      caseC   two     lox22_meja_14d_TechRep.2        24.2
>
> Only to get this error message again:
> > qPCR.example<-file.path(path, "refinedCtData2.txt")
> > qPCRBatch.qPCR=read.qPCR(qPCR.example)
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>  :
>   line 1 did not have 6 elements
>
> Any suggestions?
>
> Thanks,
> 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] NormqPCR_1.4.0      ReadqPCR_1.4.0      affy_1.36.1
> BiocInstaller_1.8.3 HTqPCR_1.12.0       limma_3.14.0
> [7] RColorBrewer_1.0-5  Biobase_2.18.0      BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.26.0         gdata_2.12.0          gplots_2.11.0
> gtools_2.7.0          preprocessCore_1.20.0 stats4_2.15.1
> [7] tools_2.15.1          zlibbioc_1.4.0
> >
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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