[BioC] ArrayQualityMetrics: Problem with labels in plots
Audrey Kauffmann
audrey at ebi.ac.uk
Tue Nov 3 13:05:15 CET 2009
Hi Elliott,
I did not manage to reproduce the error you got, so I have a few
questions. Is the object rg an RGList? Does it have 4 channels (red
foreground and background and green foreground and background)? Can you
show how you go from rg to ma?
Hopefully I will be able to understand better what is going on and find
out what went wrong (I never saw such error before). Thank you for your
feedback, it is always useful to track down errors.
Best wishes,
Audrey
> Hi BioC,
>
> I was suffering with this problem so followed the conversation which led
to a conclusion last week.
> I have installed version 2.4.1 this morning.
> I like to run the arrayQualityMetrics on both the raw and Normalised data.
> The normalised data runs fine and I'm happy to report the labelling
issue has been resolved.
> However, something odd has occurred which I can't track.
>
>> arrayQualityMetrics(rg, "QCReport_20mg", force=TRUE,do.logtransform =
> TRUE,intgroup="Cy5", grouprep=TRUE)
> The report will be written in directory 'QCReport_20mg'.
> Error in dimnames(x) <- dn :
> length of 'dimnames' [2] not equal to array extent
>> arrayQualityMetrics(ma, "QCReportMA_20mg", force=TRUE,do.logtransform
> = FALSE,intgroup="Cy5", grouprep=TRUE)
> The report will be written in directory 'QCReportMA_20mg'.
> [[1]]
>
> [[2]]
>
> [[3]]
>
>
> The raw data now reports an error but the normalised data does not.
>
>
> This code used to run fine so I'm not sure what has changed in the new
version to prevent it.
>
> traceback shows
>
> traceback()
> 7: `colnames<-`(`*tmp*`, value = 1:4)
> 6: aqm.prepdata(expressionset, do.logtransform)
> 5: aqm.prepdata(expressionset, do.logtransform)
> 4: arrayQualityMetrics(expressionset, outdir, force, do.logtransform,
> intgroup, grouprep)
> 3: arrayQualityMetrics(expressionset, outdir, force, do.logtransform,
> intgroup, grouprep)
> 2: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE,
> do.logtransform = TRUE,
> intgroup = "Cy5", grouprep = TRUE)
> 1: arrayQualityMetrics(rg, "QCReport_20mg", force = TRUE,
> do.logtransform = TRUE,
> intgroup = "Cy5", grouprep = TRUE)
>
>
> Session Info
>
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
> other attached packages:
> [1] convert_1.20.0 marray_1.22.0 limma_2.18.3
> arrayQualityMetrics_2.4.1 affyPLM_1.20.0 preprocessCore_1.6.0
>
> [7] gcrma_2.16.0 Biostrings_2.12.10 IRanges_1.2.3
> affy_1.22.1 Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0 annotate_1.22.0 AnnotationDbi_1.6.1
> beadarray_1.12.1 DBI_0.2-4 genefilter_1.24.3 grid_2.9.0
hwriter_1.1
> [9] KernSmooth_2.23-3 lattice_0.17-26 latticeExtra_0.6-4
> RColorBrewer_1.0-2 RSQLite_0.7-3 simpleaffy_2.20.0
> splines_2.9.0 stats4_2.9.0
> [17] survival_2.35-7 tools_2.9.0 vsn_3.12.0
> xtable_1.5-5
>
>
> I think it may be related to my annotation of the files when assigning
targets which I do here
>
> targets <- readTargets(file="Targets.txt", row.names="Filename")
>
> Here is the file
>
> Filename Cy5 Cy3
> US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_1.txt AL-C1D21
> ref
> US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_2.txt AL-C1D21
> ref
> US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_3.txt AL-C1D21
> ref
> US91903684_252414410012_S01_GE2_105_Dec08_2_EH_1_4.txt AL-C1D1 ref
US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_1.txt CGE-C2D21 ref
> US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_2.txt CGE-C1D1
> ref
> US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_3.txt CGE-C1D1
> ref
> US91903684_252414410012_S01_GE2_105_Dec08_2_EH_2_4.txt CGE-C1D1
> ref
> US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_1.txt BS-C1D1 ref
US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_2.txt BS-C1D1 ref
US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_3.txt CGE-C2D21 ref
> US91903684_252414410013_S01_GE2_105_Dec08_2_EH_1_4.txt CGE-C2D21 ref
> US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_1.txt BS-C1D21
> ref
> US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_2.txt BS-C1D21
> ref
> US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_3.txt BS-C1D21
> ref
> US91903684_252414410013_S01_GE2_105_Dec08_2_EH_2_4.txt BS-C1D1 ref
US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_1.txt AL-C1D1 ref
US91903684_252414410017_S01_GE2_105_Dec08_2_EH_2_2.txt AL-C1D1 ref
>
>
> Can anyone help resolve this?
>
> Thanks
>
> Elliott
>
>
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>
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Audrey Kauffmann
EMBL - EBI
Cambridge UK
+44 (0) 1223 492 631
http://www.ebi.ac.uk/~audrey
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