Dear list,
Tried to re-analyze an HTqPCR object from last year, but my limmaCtdata command in my R file failed where it worked OK last year. Running the R code that is coming with the package using R studio I noticed that certain modifications of the HTqPCR object "raw" results in the same probem when trying to do linear modeling of microarray data. FilterCtData to remove genes with 4 or more "Undetermined" features, and change the order according to featureNames (sr.norm2 <- sr.norm[order(featureNames(sr.norm))]) both result in the same error message;
Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 192, 0
Did anyone encounter the same problems with this package and does anyone has a solution to the problem? I'd really like to reanalyze my previous data using this package, but I'm not that good in writing R script files.
> sessionInfo()
R version 3.4.0 (2017-04-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] HTqPCR_1.30.0 RColorBrewer_1.1-2 Biobase_2.36.2 BiocGenerics_0.22.1 limma_3.32.10 loaded via a namespace (and not attached): [1] gtools_3.5.0 bitops_1.0-6 affy_1.54.0 stats4_3.4.0 KernSmooth_2.23-15 BiocInstaller_1.26.1 [7] gplots_3.0.1 zlibbioc_1.22.0 gdata_2.18.0 affyio_1.46.0 preprocessCore_1.38.1 statmod_1.4.30 [13] tools_3.4.0 compiler_3.4.0 caTools_1.17.1
Cheers,
Henk