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Hi list,
I'm using the HTqPCR package to read data, set categories, normalize and so on. However, I'm having problems with the HTqPCR limma function "limmaCtData".
normFilt is a normalized and filtered qPCRset
>>show(normFilt) An object of class "qPCRset" Size: 92 features, 19 samples Feature types: Feature names: hsa-miR-140-3p-002234 hsa-miR-143-000466 hsa-miR-214-000517 ... Feature classes: Feature categories: OK, Unreliable, Undetermined Sample names: 1 2 3 ... >> limmaCtData(normFilt, design=design, contrasts=contrasts, adjust.method="fdr") #, lfc=log2(0), ndups=1, spacing=1) Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 92, 0 Calls: limmaCtData -> cbind -> cbind -> data.frame Execution halted
Has anybody experienced this problem?
Session Info is as follows:
R » sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Gentoo/Linux locale: [1] LC_CTYPE=pt_BR.utf8 LC_NUMERIC=C LC_TIME=pt_BR.utf8 LC_COLLATE=pt_BR.utf8 LC_MONETARY=pt_BR.utf8 [6] LC_MESSAGES=pt_BR.utf8 LC_PAPER=pt_BR.utf8 LC_NAME=pt_BR.utf8 LC_ADDRESS=pt_BR.utf8 LC_TELEPHONE=pt_BR.utf8 [11] LC_MEASUREMENT=pt_BR.utf8 LC_IDENTIFICATION=pt_BR.utf8 attached base packages: [1] parallel stats graphics grDevices datasets utils methods base other attached packages: [1] xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-8 HTqPCR_1.28.0 limma_3.30.13 RColorBrewer_1.1-2 Biobase_2.34.0 [8] BiocGenerics_0.20.0 BiocInstaller_1.24.0 setwidth_1.0-4 colorout_1.1-0 loaded via a namespace (and not attached): [1] gtools_3.5.0 bitops_1.0-6 affy_1.52.0 stats4_3.3.2 KernSmooth_2.23-15 gplots_3.0.1 zlibbioc_1.20.0 [8] gdata_2.18.0 affyio_1.44.0 preprocessCore_1.36.0 tools_3.3.2 caTools_1.17.1