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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > [[alternative HTML version deleted]]