Question: HTqPCR: number of samples, number of features
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gravatar for alessandro brozzi
7.2 years ago by
European Union
alessandro brozzi120 wrote:
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. 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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ADD COMMENTlink modified 7.2 years ago by Heidi Dvinge2.0k • written 7.2 years ago by alessandro brozzi120
Answer: HTqPCR: number of samples, number of features
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gravatar for Heidi Dvinge
7.2 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 7.2 years ago by Heidi Dvinge2.0k
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]]
ADD REPLYlink written 7.2 years ago by alessandro brozzi120
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