[BioC] Plate config for 1536 plate into cellHTS2

[Joseph Barry]

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.