Problems creating a qPCRset object in "HTqPCR"
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@peter-davidsen-4584
Last seen 8.5 years ago
Dear List, I'm trying to use the "HTqPCR" BioC package to analyze "SDS-format" qPCR data (ran 384-well plates on an ABI 7900HT). I have 20 different txt-files (in SDS-format) as I quantified 20 different miRNAs (thus, only one GOI per plate/file) - on each plate I have 33 samples in triplicate. Example of how my txt-files are organized: SDS 2.3 AQ Results 1.0 Filename 05.08.2010_miR-208b_Ceramide_1-33 PlateID Assay Type Absolute Quantification Run DateTime 05/08/10 14:28:11 Operator ThermalCycleParams Sample Information Well Sample Name Detector Name Reporter Task Ct.... 82 D10 miR-208b FAM Unknown 31.154957 83 D11 miR-208b FAM Unknown 30.56075 84 D12 miR-208b FAM Unknown 30.617414 85 D13 miR-208b FAM Unknown 29.638447 86 D14 miR-208b FAM Unknown 29.873674 87 D15 miR-208b FAM Unknown 29.974564 88 D16 miR-208b FAM Unknown 32.324512 89 D17 miR-208b FAM Unknown 31.65119 90 D18 miR-208b FAM Unknown 32.567085 91 D19 miR-208b FAM Unknown 30.977701 92 D20 miR-208b FAM Unknown 31.459805 The command I run is: # Load HTqPCR package library("HTqPCR") # Set working dir path <- setwd('C:/Documents and Settings/RH35363/Dokumenter/Dropbox/Ceramide Study/SDS-files') exFiles <- read.delim(file.path(path, "files.txt")) # "files.txt" contains a list with the file names of my 20 txt-files raw <- readCtData(files=exFiles$File, path=path, n.features = 99, flag = NULL, feature = 3, type = 5, position = 2, Ct = 6, n.data = 33, na.value = 40, header=T, SDS = FALSE, skip = 10, sep='\t') # Since my headers are apparently different/in a different order, I have set these parameters accordingly. I've set SDS=FALSE as my SDS software generated txt-files lack a "#" in the first column. And the error I get is: Error in `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined") : only logical matrix subscripts are allowed in replacement In addition: Warning messages: 1: In readCtData(files = "05.08.2010_miR-208b_Ceramide_1-33.txt", path = NULL, : 99 gene names (rows) expected, got 1132 2: In matrix(sample[, Ct], ncol = n.data[i]) : data length [116] is not a sub-multiple or multiple of the number of columns [33] With the traceback information as follows: > traceback() 4: stop("only logical matrix subscripts are allowed in replacement") 3: `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined") 2: `[<-`(`*tmp*`, undeter, value = "Undetermined") 1: readCtData(files = exFiles$File, path = path, n.features = 99, flag = NULL, feature = 3, type = 5, position = 2, Ct = 6, n.data = 33, na.value = 40, header = T, SDS = FALSE, skip = 10, sep = "\t") I tried to change the "n.data" parameter from 33 to 1, this removed the error: raw <- readCtData(files=exFiles$File, path=path, n.features = 99, flag = NULL, feature = 3, type = 5, position = 2, + Ct = 6, n.data = 1, header=T, SDS = FALSE, skip = 10, sep='\t') Warning message: In readCtData(files = exFiles$File, path = path, n.features = 93, : 99 gene names (rows) expected, got 1132 Thus, it seems to me like I'm loading my data in the wrong way. Any thoughts/suggestions on how to solve this problem are welcomed! > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] HTqPCR_1.4.0 limma_3.6.9 RColorBrewer_1.0-2 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.1 affyio_1.18.0 gdata_2.8.2 [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.12.0 Kind regards, Peter
HTqPCR HTqPCR • 1.8k views
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Entering edit mode
@peter-davidsen-4584
Last seen 8.5 years ago
Dear List, I'm trying to use the "HTqPCR" BioC package to analyze "SDS-format" qPCR data (ran 384-well plates on an ABI 7900HT). I have 20 different txt-files (in SDS-format) as I quantified 20 different miRNAs (thus, only one GOI per plate/file) - on each plate I have 33 samples in triplicate. Example of how my txt-files are organized: SDS 2.3 AQ Results 1.0 Filename 05.08.2010_miR-208b_Ceramide_1-33 PlateID Assay Type Absolute Quantification Run DateTime 05/08/10 14:28:11 Operator ThermalCycleParams Sample Information Well Sample Name Detector Name Reporter Task Ct.... 82 D10 miR-208b FAM Unknown 31.154957 83 D11 miR-208b FAM Unknown 30.56075 84 D12 miR-208b FAM Unknown 30.617414 85 D13 miR-208b FAM Unknown 29.638447 86 D14 miR-208b FAM Unknown 29.873674 87 D15 miR-208b FAM Unknown 29.974564 88 D16 miR-208b FAM Unknown 32.324512 89 D17 miR-208b FAM Unknown 31.65119 90 D18 miR-208b FAM Unknown 32.567085 91 D19 miR-208b FAM Unknown 30.977701 92 D20 miR-208b FAM Unknown 31.459805 The command I run is: # Load HTqPCR package library("HTqPCR") # Set working dir path <- setwd('C:/Documents and Settings/RH35363/Dokumenter/Dropbox/Ceramide Study/SDS-files') exFiles <- read.delim(file.path(path, "files.txt")) # "files.txt" contains a list with the file names of my 20 txt-files raw <- readCtData(files=exFiles$File, path=path, n.features = 99, flag = NULL, feature = 3, type = 5, position = 2, Ct = 6, n.data = 33, na.value = 40, header=T, SDS = FALSE, skip = 10, sep='\t') # Since my headers are apparently different/in a different order, I have set these parameters accordingly. I've set SDS=FALSE as my SDS software generated txt-files lack a "#" in the first column. And the error I get is: Error in `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined") : only logical matrix subscripts are allowed in replacement In addition: Warning messages: 1: In readCtData(files = "05.08.2010_miR-208b_Ceramide_1-33.txt", path = NULL, : 99 gene names (rows) expected, got 1132 2: In matrix(sample[, Ct], ncol = n.data[i]) : data length [116] is not a sub-multiple or multiple of the number of columns [33] With the traceback information as follows: > traceback() 4: stop("only logical matrix subscripts are allowed in replacement") 3: `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined") 2: `[<-`(`*tmp*`, undeter, value = "Undetermined") 1: readCtData(files = exFiles$File, path = path, n.features = 99, flag = NULL, feature = 3, type = 5, position = 2, Ct = 6, n.data = 33, na.value = 40, header = T, SDS = FALSE, skip = 10, sep = "\t") I tried to change the "n.data" parameter from 33 to 1, this removed the error: raw <- readCtData(files=exFiles$File, path=path, n.features = 99, flag = NULL, feature = 3, type = 5, position = 2, + Ct = 6, n.data = 1, header=T, SDS = FALSE, skip = 10, sep='\t') Warning message: In readCtData(files = exFiles$File, path = path, n.features = 93, : 99 gene names (rows) expected, got 1132 Thus, it seems to me like I'm loading my data in the wrong way. Any thoughts/suggestions on how to solve this problem are welcomed! > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] HTqPCR_1.4.0 limma_3.6.9 RColorBrewer_1.0-2 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.1 affyio_1.18.0 gdata_2.8.2 [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.12.0 Kind regards, Peter
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