affycoretools - improve error message in annotateEset(ExpressionSet, AffyExpressionPDInfo)
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Entering edit mode
@gerhard-thallinger-1552
Last seen 6 weeks ago
Austria

When trying to annotate an ExpressionSet with annotateEset() specifying an AffyExpressionPDInfo package without an annotation object, the following error message is displayed:

  Error: There is no annotation object provided with the x package.

Working example:

  library(affycoretools)
  library(pd.mirna.4.0)

  data(sample.ExpressionSet)
  eset <- sample.ExpressionSet
  eset.ann <- annotateEset(eset, pd.mirna.4.0)

  # ... yes, I know that this is not the correct package for annotating the particular eset,
  # but it serves the purpose

The error itself is expected, it would be helpful, if 'x' is replaced by the package name specified:

  Error: There is no annotation object provided with the 'pd.mirna.4.0' package.

R and Bioconductor environment:

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pd.mirna.4.0_3.12.0  DBI_1.1.1            oligo_1.58.0         oligoClasses_1.56.0 
 [5] RSQLite_2.2.8        Biostrings_2.62.0    GenomeInfoDb_1.30.0  XVector_0.34.0      
 [9] IRanges_2.28.0       S4Vectors_0.32.2     affycoretools_1.66.0 Biobase_2.54.0      
[13] BiocGenerics_0.40.0
affycoretools • 900 views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 10 minutes ago
United States

Thanks for pointing out the bug. Fixed in devel.

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