Problem with ArrayQualityMetrics PCA plot
Entering edit mode
michael.s • 0
Last seen 26 days ago

I created an ArrayQualityMetrics report of a Large ExpressionSet. The problem is that when I move the mouse over the points of the PCA plot , the corresponding array’s metadata are not displayed in the table to the right of the plot, as they are supposed to be. Also, the data points are not responsive as they should be, when they are clicked. Nor do they correspond when the sample boxes are checked (in the initial samples table). I have tried Chrome and Firefox and the problem remains.

The report is working properly here, but this report was created by using an older package version (3.11.0).

Does anyone have any ideas about this? Thank you.

arrayQualityMetrics(expressionset = data, outdir = "Report_final_dataset", force = TRUE, intgroup = c("condition", "batch"))

sessionInfo( )

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253   
[3] LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C                 
[5] LC_TIME=Greek_Greece.1253    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hgu133acdf_2.18.0          ALLMLL_1.34.0             
 [3] affy_1.72.0                Biobase_2.54.0            
 [5] BiocGenerics_0.40.0        arrayQualityMetrics_3.50.0
 [7] sva_3.42.0                 BiocParallel_1.28.1       
 [9] genefilter_1.76.0          mgcv_1.8-38               
[11] nlme_3.1-153               limma_3.50.0      
arrayQualityMetrics • 125 views
Entering edit mode
Last seen 7 days ago
EMBL European Molecular Biology Laborat…

Hi Michael,

The interactivity in arrayQualityMetrics works by injecting JavaScript into the SVG produced by R, using assumptions that are very brittle - across versions of R and packages, and even across different system environments. The software is now around 10 years old, and the interactive plotting aspects are really not worth fixing, as there are now much better approaches (plotly, shiny...)

Could you try the MatrixQCvis package? It uses a more modern shiny-based approach, .

HTH Wolfgang


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