[BioC] Plate config for 1536 plate into cellHTS2

Rossella Rispoli [guest] guest at bioconductor.org
Thu Aug 21 14:34:30 CEST 2014

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,


 -- output of sessionInfo(): 

R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[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      

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