[BioC] ArrayQualityMetrics: Problem with labels in plots

elliott harrison e.harrison at epistem.co.uk
Tue Nov 3 15:04:59 CET 2009


HI Audrey,
Thanks for getting back to me.

rg is an rglist with 4 channels

> class(rg)
[1] "RGList"
attr(,"package")
[1] "limma"
> summary(rg)
        Length  Class      Mode     
G       1133568 -none-     numeric  
Gb      1133568 -none-     numeric  
R       1133568 -none-     numeric  
Rb      1133568 -none-     numeric  
targets       3 data.frame list     
genes        11 data.frame list     
source        1 -none-     character
printer       4 -none-     list     


This is the procedure used to get from rg to ma

rgb <- backgroundCorrect(rg, method="normexp",offset=50)
ma <- normalizeWithinArrays(rgb, method="loess")
ma <-  normalizeBetweenArrays(ma, method="quantile")


Hope that helps

Thanks 

Elliott

-----Original Message-----
From: Audrey Kauffmann [mailto:audrey at ebi.ac.uk] 
Sent: 03 November 2009 12:05
To: elliott harrison
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] ArrayQualityMetrics: Problem with labels in plots

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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Audrey Kauffmann
EMBL - EBI
Cambridge UK
+44 (0) 1223 492 631
http://www.ebi.ac.uk/~audrey




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