[BioC] Taking out a plate from a HTS analysis

[Rossella Rispoli]

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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