[BioC] Taking out a plate from a HTS analysis

[Joseph Barry]

Yes you can use the screenLog file to exclude plates. You cannot use regular expressions for this as for the plateConf file however, but you can automatically generate one with the following or similar:

library(cellHTS2)
myScreenLog <- data.frame(Plate=rep(4, 1536),
    Well=convertWellCoordinates(1:1536, type="1536")$letnum, Flag=NA,
    Comment="Contamination")
write.table(myScreenLog, file="myScreenlog.txt", row.names=FALSE, col.names=TRUE, quote=FALSE, sep="\t")

In the end this will populate the assayData array with NAs for plate 4. I personally prefer this option since it is useful to keep track of what plates were excluded for what reason. Another advantage is that you retain the original plate ids.

Best wishes,
Joseph

On 21 Aug 2014, at 14:59, Rossella Rispoli <rossella.rispoli at gmail.com> wrote:

> Thanks for your replay,
> yes I did but I still got the error. That's way I changed the plateList order. 
> 
> I knew about the screenLog file to annotate problem wells that you wish to exclude from the analysis, can you use it to annotate plate to esclude as well????
> 
> Many thanks,
> 
> Rossella
> 
> 
> 2014-08-21 13:58 GMT+01:00 Rossella Rispoli <rossella.rispoli at gmail.com>:
> Thanks for your replay,
> yes I did but I still got the error. That's way I changed the plateList order. 
> 
> I knew about the screenLog file to annotate problem wells that you wish to exclude from the analysis, can you use it to annotate plate to esclude as well????
> 
> Many thanks,
> 
> Rossella 
> 
> 
> 
> 
> 2014-08-21 13:49 GMT+01:00 Joseph Barry <joseph.barry at embl.de>:
> 
> Dear Rossella,
> 
> Thank you for your inquiry. Can you first please confirm that you have reduced the specified number of plates in your plateConf.txt file from 17 to 16 (that the header reads “Plates: 16”). This number should match the number of plates you are reading in.
> 
> Also note that you can use the screen log file to annotate problem wells that you wish to exclude from the analysis (see ?configure for more details).
> 
> Best wishes,
> Joseph
> 
> 
> On 21 Aug 2014, at 14:19, Rossella at embl-heidelberg.de wrote:
> 
> > 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,
> >
> > 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.
> 
> 
> 
> 
> -- 
> ------------------------------------------------------
> Rossella Rispoli,
> High Throughput Screening lab
> Cancer Research UK
> 44 Lincoln's Inn fields
> London WC2A 3LY UK
> Tel No. +44 (0)207 269 3151
> Fax No. +44 (0)207 269 3581
> ------------------------------------------------------
> 
> 
> 
> -- 
> ------------------------------------------------------
> Rossella Rispoli,
> High Throughput Screening lab
> Cancer Research UK
> 44 Lincoln's Inn fields
> London WC2A 3LY UK
> Tel No. +44 (0)207 269 3151
> Fax No. +44 (0)207 269 3581
> ------------------------------------------------------


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