[BioC] Taking out a plate from a HTS analysis

Rossella Rispoli [guest] guest at bioconductor.org
Thu Aug 21 14:19:43 CEST 2014

Dear all

A very simple question question. 

I'm analysing some HTS data withe 1536 plate and the library is made by 17 plates.
I had the need to remove one plate from the analysis (plate 4). 
When I tried to run the analysis again changing just the plateList file, removing the rows releted to the three replicate of plate 4, I got an error sayng: 

Error in (function (filename, path, nrPlate, nrWpP, ...)  : 
  in 'plateConf.txt', the number of plates 
 specified in the header line 'Plates:' is 17 but I expected 16.

 and I realised that the readPlateList function count a total of 17 plate also if you remove same in the middle (maybe because I toke the maximum from the plateList). 

That's means that I needed to update the plateList file in a way that the number of the plates was ending to 16. 
I udated the GeneAnnotation file as well removing all annotation for plate 4 and udating the plate number from the plate 5 to 17 decreasing avery platenumber. 

In this way I was able to do my analysis. 

I was wondering is there any other simple way to do it? 

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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