hi Heidi,

with:

n.data=40
n.features=96

it works fine.

thank you very much!
Alex

On Mon, Sep 10, 2012 at 2:07 AM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:

> 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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