[BioC] HTqPCR: number of samples, number of features

[Heidi Dvinge]

Hi Alex,

> hi,
> I've been given an SDS raw file (see below) which contains embedded 10
> cards of 348 wells each.
> The genes are totally 48 and each card has 4 samples so totally 40
> samples.
> If I am correct n.features should be = 3480 and the n.data (the number of
> samples that are present in each file) should be = 40.
>
Actually, the number of features should be those present per array, not
per file (there's a typo in the documentation; I'll get that fixed).

In this case, you may have to read in the data with n.features=384 and
n.data=10, and then use e.g. changeCtLayout to re-format your qPCRset
object to take the 4 samples per array into account. This re-formatting
may need to be either before or after normalisation, depending on your
data.

You can perhaps also try reading it in that way directly, using n.data=40
and n.features=96 (I assume each of your 48 genes are present twice;
otherwise the numbers don't add up).

Does that work? If not, I'll need to look under the hood of readCtData.

\Heidi

> But reading in the file I've got the following error:
>
>  raw <- readCtData(files = "./raw/Hs/cards+1-10+21-4-09.txt",
> +                   n.features = 3840,
> +                   format = "SDS",
> +                   n.data=40)
> Error in `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined") :
>   only logical matrix subscripts are allowed in replacement
> Warning message:
> In matrix(sample[, column.info[["Ct"]]], ncol = n.data[i]) :
>   data length [5765] is not a sub-multiple or multiple of the number of
> rows [145]
>
>
> any suggestions?
>
> thanks in advance,
> alex
>
> -------------- SDS file -----------------------
>
> SDS 2.1RQ Results    1.0
> Filename    cards 1-10  21-4-09.sdm
> Assay Type    RQ Study
> EmbeddedFile    card1 16-4-09
> Run DateTime    Thu Apr 16 10:59:02 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card10  21-4-09
> Run DateTime    Tue Apr 21 08:56:39 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card2 16-4-09
> Run DateTime    Thu Apr 16 13:06:51 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card3 17-4-09
> Run DateTime    Fri Apr 17 09:12:29 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card4 17-4-09
> Run DateTime    Fri Apr 17 11:16:29 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card5 17-4-09
> Run DateTime    Fri Apr 17 13:53:36 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card6 17-4-09
> Run DateTime    Fri Apr 17 15:52:02 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card7 20-4-09
> Run DateTime    Mon Apr 20 09:13:39 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card8 20-4-09
> Run DateTime    Mon Apr 20 11:30:13 CEST 2009
> Operator
> ThermalCycleParams
> EmbeddedFile    card9 20-4-09
> Run DateTime    Mon Apr 20 13:57:32 CEST 2009
> Operator
> ThermalCycleParams
>
> #Well    PlateID    Sample    Detector    Task    Ct    delta Rn    delta
> Ct    Ct Avg    Ct SD    Avg Delta Ct    delta Ct SD    Endo Ct Avg
> Endo
> Ct SD    delta delta Ct    RQ    RQ Min    RQ Max    Baseline Type
> Baseline Start    Baseline Stop    Threshold Type    Threshold
> Instrument    Outlier    Filename
> 1        human promyel    HEL308-Hs00431095_m1    Target    29.939869
> 3.8580723        30.092875    0.1530056    18.400938    0.29772463
> 11.6919365    0.25540018    0.8945656    0.53790915    0.22135419
> 1.307164    Automatic            Automatic    0.46168146    200978
> card1 16-4-09
> 2        human promyel    ZBTB7C-Hs00402493_g1    Target    Undetermined
> -0.0025281906        40.0    0.0    28.308064        11.6919365
> 0.25540018                    Automatic            Automatic    0.2
> 200978        card1 16-4-09
> 3        human promyel    CPNE8-Hs00402394_m1    Target    33.381207
> 1.2499179        32.37199    1.0092154    20.680054    1.0410306
> 11.6919365    0.25540018    -0.99511147    1.9932345    0.08936897
> 44.455967    Automatic            Automatic    0.22997451    200978
> card1 16-4-09
> 4        human promyel    JMJD3-Hs00389738_m1    Target    29.998976
> 2.7376282        29.691463    0.30751133    17.999527    0.39974052
> 11.6919365    0.25540018    1.2906017    0.4087805    0.124089554
> 1.3466202    Automatic
> ......etc etc......
>
> 	[[alternative HTML version deleted]]
>
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