Dear all, I'm trying to read raw data from TaqMan TLDA cards. The Ct values were extracted from SDS file with ExpressionSuite software. I tried to adjust the files according to the example data provided in the package so currently I have the data file which looks the following and contains 60 samples: flag feature type position Ct sample Passed hsa-let-7a-000377 Target A1 27.456 Sample1 Passed hsa-miR-10b-002218 Target A10 30.314 Sample1 Passed U6 snRNA-001973 Endogenous Control A11 30.115 Sample1 Passed U6 snRNA-001973 Endogenous Control A12 29.226 Sample1 Passed hsa-miR-15a-000389 Target A13 30.238 Sample1 the files.txt contains only the name of the file above and header "File". When trying to read the data I get the following error: > files <- read.delim("D:/Magdalena/MicroRNA/Results/Pilot/Card A/HTqPCR_files/files.txt") > raw <- readCtData(files=files$File, path='D:/Magdalena/MicroRNA/Results/Pilot/Card A/HTqPCR_files', n.features = 384, header = TRUE, format="SDS", column.info=list(flag=1, feature=2, type=3, position=4, Ct=5), n.data = 60, samples = sample, na.value = 40) Warning messages: 1: In FUN(newX[, i], ...) : NAs introduced by coercion 2: In readCtData(files = files$File, path = "D:/Magdalena/MicroRNA/Results/Pilot/Card A/HTqPCR_files", : Not enough sample names provided; using Sample1, Sample2, ... instead 3: In readCtData(files = files$File, path = "D:/Magdalena/MicroRNA/Results/Pilot/Card A/HTqPCR_files", : One or more samples contain NAs. Consider replacing these with e.g. Ct=40 now. I definitely don't have any NAs in my file (also changed any "Undetermined" to 40), and in the sample column all the samples names are listed. I can't find the mistake in my code. I would be very grateful for help. Best wishes, Magdalena > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] HTqPCR_1.12.0 limma_3.14.4 RColorBrewer_1.0-5 [4] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affy_1.36.1 affyio_1.26.0 [3] BiocInstaller_1.8.3 gdata_2.12.0.1 [5] gplots_2.11.0 gtools_2.7.1 [7] preprocessCore_1.20.0 stats4_2.15.2 [9] tools_2.15.2 zlibbioc_1.4.0 [[alternative HTML version deleted]]