Dear all A very simple question. I'm analysing some HTS data withe 1536 plate. But I got some trobule to understand the format of the plateConfig file for the 1536 plate. In my case for example I need to specifies the controls configuration as follows: AtoH column 1-3 RF AtoH column 4-8 RF plus TGFB ACtoAF column 1-3 UBB ACtoAF column 4-8 UBB plus TGFB Can someone can tell me how to write it in a regular expression acceptble from the CellHTS2? I tried in differten way but in the end I got success just in this way: * ^A0[1-3] RF_NoTGFB * ^B0[1-3] RF_NoTGFB * ^C0[1-3] RF_NoTGFB * ^D0[1-3] RF_NoTGFB * ^E0[1-3] RF_NoTGFB * ^F0[1-3] RF_NoTGFB * ^G0[1-3] RF_NoTGFB * ^H0[1-3] RF_NoTGFB * ^A0[4-8] RF_TGFB * ^B0[4-8] RF_TGFB * ^C0[4-8] RF_TGFB * ^D0[4-8] RF_TGFB * ^E0[4-8] RF_TGFB * ^F0[4-8] RF_TGFB * ^G0[4-8] RF_TGFB * ^H0[4-8] RF_TGFB * ^AC0[1-3] UBB_NoTGFB * ^AD0[1-3] UBB_NoTGFB * ^AE0[1-3] UBB_NoTGFB * ^AF0[1-3] UBB_NoTGFB * ^AC0[4-8] UBB_TGFB * ^AD0[4-8] UBB_TGFB * ^AE0[4-8] UBB_TGFB * ^AF0[4-8] UBB_TGFB Any help will be very much appreciated Thanks in advances, Rossella -- output of sessionInfo(): R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] RODBC_1.3-10 cellHTS2_2.28.0 locfit_1.5-9.1 hwriter_1.3 vsn_3.32.0 splots_1.30.0 genefilter_1.46.1 Biobase_2.24.0 BiocGenerics_0.10.0 RColorBrewer_1.0-5 loaded via a namespace (and not attached): [1] affy_1.42.3 affyio_1.32.0 annotate_1.42.1 AnnotationDbi_1.26.0 BiocInstaller_1.14.2 Category_2.30.0 DBI_0.2-7 DEoptimR_1.0-1 GenomeInfoDb_1.0.2 graph_1.42.0 GSEABase_1.26.0 [12] IRanges_1.22.10 lattice_0.20-29 limma_3.20.8 MASS_7.3-33 Matrix_1.1-4 mvtnorm_1.0-0 pcaPP_1.9-49 prada_1.40.0 preprocessCore_1.26.1 RBGL_1.40.1 robustbase_0.91-1 [23] rrcov_1.3-4 RSQLite_0.11.4 splines_3.1.1 stats4_3.1.1 survival_2.37-7 tools_3.1.1 XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.

Dear Rossella, Your plateConf looks pretty good. You can make it a bit more concise with the following: * ^[A-H]0[1-3] RF_NoTGFB * ^[A-H]0[4-8] RF_TGFB * ^A[C-F]0[1-3] UBB_NoTGFB * ^A[C-F]0[4-8] UBB_TGFB The ^ is important to avoid any confused matches between e.g. A and AA. Best wishes, Joseph On 21 Aug 2014, at 14:34, Rossella at embl-heidelberg.de wrote: > Dear all > > A very simple question. > > I'm analysing some HTS data withe 1536 plate. > But I got some trobule to understand the format of the plateConfig file for the 1536 plate. > > In my case for example I need to specifies the controls configuration as follows: > > AtoH column 1-3 RF > AtoH column 4-8 RF plus TGFB > ACtoAF column 1-3 UBB > ACtoAF column 4-8 UBB plus TGFB > > Can someone can tell me how to write it in a regular expression acceptble from the CellHTS2? > I tried in differten way but in the end I got success just in this way: > > * ^A0[1-3] RF_NoTGFB > * ^B0[1-3] RF_NoTGFB > * ^C0[1-3] RF_NoTGFB > * ^D0[1-3] RF_NoTGFB > * ^E0[1-3] RF_NoTGFB > * ^F0[1-3] RF_NoTGFB > * ^G0[1-3] RF_NoTGFB > * ^H0[1-3] RF_NoTGFB > * ^A0[4-8] RF_TGFB > * ^B0[4-8] RF_TGFB > * ^C0[4-8] RF_TGFB > * ^D0[4-8] RF_TGFB > * ^E0[4-8] RF_TGFB > * ^F0[4-8] RF_TGFB > * ^G0[4-8] RF_TGFB > * ^H0[4-8] RF_TGFB > * ^AC0[1-3] UBB_NoTGFB > * ^AD0[1-3] UBB_NoTGFB > * ^AE0[1-3] UBB_NoTGFB > * ^AF0[1-3] UBB_NoTGFB > * ^AC0[4-8] UBB_TGFB > * ^AD0[4-8] UBB_TGFB > * ^AE0[4-8] UBB_TGFB > * ^AF0[4-8] UBB_TGFB > > Any help will be very much appreciated > > Thanks in advances, > > Rossella > > > > > > -- output of sessionInfo(): > > R version 3.1.1 (2014-07-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RODBC_1.3-10 cellHTS2_2.28.0 locfit_1.5-9.1 hwriter_1.3 vsn_3.32.0 splots_1.30.0 genefilter_1.46.1 Biobase_2.24.0 BiocGenerics_0.10.0 RColorBrewer_1.0-5 > > loaded via a namespace (and not attached): > [1] affy_1.42.3 affyio_1.32.0 annotate_1.42.1 AnnotationDbi_1.26.0 BiocInstaller_1.14.2 Category_2.30.0 DBI_0.2-7 DEoptimR_1.0-1 GenomeInfoDb_1.0.2 graph_1.42.0 GSEABase_1.26.0 > [12] IRanges_1.22.10 lattice_0.20-29 limma_3.20.8 MASS_7.3-33 Matrix_1.1-4 mvtnorm_1.0-0 pcaPP_1.9-49 prada_1.40.0 preprocessCore_1.26.1 RBGL_1.40.1 robustbase_0.91-1 > [23] rrcov_1.3-4 RSQLite_0.11.4 splines_3.1.1 stats4_3.1.1 survival_2.37-7 tools_3.1.1 XML_3.98-1.1 xtable_1.7-3 zlibbioc_1.10.0 > > > -- > Sent via the guest posting facility at bioconductor.org.