[BioC] ArrayQualityMetrics: Problem with labels in plots

[elliott harrison]

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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