HTqPCR, changeCtLayout is mislabeling the rows and is unable to return a qPCRset object
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I am having problems reformatting my data. My data has several samples on one plate, so I am reading in using the format = "plain" options, and then calling changeCtLayout() to reformat it. I am reading in a 96 well plate that is organized as a 1x84 matrix (several wells not used). For the sake of detail I will be very verbose, and the first few lines of my files are at the bottom of my post. temp <- readCtData(file = "Plate1.txt", path = path, n.features = 84, n.data =1, column.info = list(flag = 3, feature = 5, type = 4, Ct = 6, position =1), format = "plain", header = TRUE) And this works well. The vector that associates the features rows with samples is stored in a file read in by: samples <- read.delim(myFile, header = TRUE, sep = "\t", stringsAsFactors = FALSE)[,"Sample"] > head(samples) [1] "Repl_d4" "Repl_d4" "Repl_d4" "Repl_d4" "Repl_d4" "Repl_d4" I call: changeCtLayout(temp, sample.order = samples) Error in function (storage.mode = c("lockedEnvironment", "environment", : 'AssayData' elements with different rowNames Setting my qPCRset temp to 'q' and my samples vector to 'sample.order' and following the code for the changeCtLayout() function, I found that the error occurs when the rownames are assigned for the variables castnew, flagsnew, and Xnew when they are merged using the new("qPCRset", exprs...) function. >rownames(Xnew) [1] "Actin" "EF" "FRO3" "FSD1" "CSD1" "FER4" "Actin.1" "EF.1" "FRO3.1" "FSD1.1" "CSD1.1" "FER4.1" [13] "Actin.2" "EF.2" "FRO3.2" "FSD1.2" "CSD1.2" "FER4.2" "FSD2" "FSD2.1" "FSD2.2" >rownames(catsnew) [1] "Actin.1" "EF.1" "FRO3.1" "FSD1.1" "CSD1.1" "FER4.1" "Actin.3" "EF.3" "FRO3.3" "FSD1.3" "CSD1.3" "FER4.3" [13] "Actin.5" "EF.5" "FRO3.5" "FSD1.5" "CSD1.5" "FER4.5" "FSD2.6" "FSD2.7" "FSD2.8" > all.equal(rownames(catsnew), rownames(flagsnew)) [1] TRUE cats <- split(as.data.frame(featureCategory(q)), sample.order) looking at the rows of the matrices in cats, all of the variable present in rownames(Xnew) and rownames(catsnew) are present. But when: catsnew <- do.call("cbind", cats) the rownames get mixed up. Thank you for any and all help! Samuel the object temp > temp An object of class "qPCRset" Size: 84 features, 1 samples Feature types: Feature names: Actin EF FRO3 ... Feature classes: Feature categories: OK Sample names: Plate1 ... > head(read.delim(myFile), 20) position Sample flag type feature Ct 1 A1 Repl_d4 Passed HouseKeeper Actin 28.0867 2 A2 Repl_d4 Passed HouseKeeper EF 20.8426 3 A3 Repl_d4 Passed Exp FRO3 21.7977 4 A4 Repl_d4 Passed Exp FSD1 16.0370 5 A5 Repl_d4 Passed Exp CSD1 17.4107 6 A6 Repl_d4 Passed Exp FER4 20.2024 7 A7 minusFe_d4 Passed HouseKeeper Actin 29.3098 8 A8 minusFe_d4 Passed HouseKeeper EF 23.0904 9 A9 minusFe_d4 Passed Exp FRO3 22.3609 10 A10 minusFe_d4 Passed Exp FSD1 22.8463 11 A11 minusFe_d4 Passed Exp CSD1 17.0752 12 A12 minusFe_d4 Passed Exp FER4 21.7814 13 B1 Repl_d4 Passed HouseKeeper Actin 28.9077 14 B2 Repl_d4 Passed HouseKeeper EF 28.5527 15 B3 Repl_d4 Passed Exp FRO3 22.6598 16 B4 Repl_d4 Passed Exp FSD1 17.5561 17 B5 Repl_d4 Passed Exp CSD1 18.9919 18 B6 Repl_d4 Passed Exp FER4 19.9053 19 B7 minusFe_d4 Passed HouseKeeper Actin 28.9616 20 B8 minusFe_d4 Passed HouseKeeper EF 22.0134 -- output of sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 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_1.12.0 limma_3.14.3 RColorBrewer_1.0-5 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 gdata_2.12.0 gplots_2.11.0 [6] gtools_2.7.0 preprocessCore_1.20.0 stats4_2.15.2 tools_2.15.2 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
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