[BioC] Taking out a plate from a HTS analysis
Rossella Rispoli [guest]
guest at bioconductor.org
Thu Aug 21 14:19:43 CEST 2014
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)
attached base packages:
 grid parallel stats graphics grDevices utils datasets methods base
other attached packages:
 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):
 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
 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
 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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