Dear list, dear Heidi, I performed a high-throughput analysis with the ABS TaqMan Open Array qPCR System, format 112- so ending up with 112 genes analysed in 454 samples(*2, technical replicates). One Run can be performed with up to 3 chips (the number of chips varies in my Runs) and I performed 16 Runs in total- taking all Runs together with /rbind/ I end up with one file with 101697 rows (so 112*908) including the header (Output.txt)- it is sorted as already shown in several examples online: Sample Gene Reps S1 Gene1 Rep1 S1 Gene1 Rep2 S1 Gene2 Rep1 S1 Gene2 Rep2 ....and so on.. ...and having the same format structure (regarding column names and column content) as the Open Array example data provided in the package. When I try to read in the Ct Data as follows, I always get the error code shown below: > raw2 <- readCtData("Output.txt",n.features=112,n.data=908,format="OpenArray",p ath="./", + column.info=list(flag="ThroughHole.Outlier", feature="Assay.Assay.ID", type="Assay.Assay.Type", position="ThroughHole.Address", Ct="ThroughHole.Ct")) Fehler in `$<-.data.frame`(`*tmp*`, "ThroughHole.Outlier", value = character(0)) : replacement has 0 rows, data has 101696 > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] HTqPCR_1.10.0 limma_3.12.3 RColorBrewer_1.0-5 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 BiocInstaller_1.4.9 gdata_2.12.0 gplots_2.11.0 [6] gtools_2.7.0 preprocessCore_1.18.0 stats4_2.15.1 tools_2.15.1 zlibbioc_1.2.0 Since I am far away from being fluent in R, I still don't know what the problem is- I tried nearly EVERYTHING now: - as I don't get any kind of flags in the Open Array original output, the ThroughHole.Outlier column is filled with 'False' but removing, changing, setting flag=NULL doesn't change a thing -changing to format=plain will give the same error code, even when flag=NULL I still don't have a clue if my data structure causes the main problem, but how to solve this? I would appreciate ANY help regarding this problem. Thanks a lot in advance, Katharina -- ><(((*> ><(((*> ><(((*> ><(((*> Katharina Michael MSc Marine Biology Katharina.Michael@awi.de [[alternative HTML version deleted]]