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In subsetGenes.xSeries, when, for a given key value (e.g., gene symbol), more than one occurrence is found in the annotation table of the xSeries (i.e., the same duplicated SYMBOL for multiple ENSG IDs) no action is taken and each entry is assigned to a different bar in the final chart, even if its name is not unique. It should be better to provide a rule to collapse statistics of genes with the same key value (e.g., keeping only the most expressed or their sum...), provided that user's "subsetting intention" is based on geneset key, rather than on (unique) ENSG IDs...
See the same problem in GOZER
The text was updated successfully, but these errors were encountered:
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Provide a rule to collapse expression of genes with the same symbol
Provide a rule to collapse expression of genes with the same key
Jun 17, 2024
Importantly, this really happens even within the restricted geneset of ion channels, as of org.Hs.eg.db v.3.18.0 (Bioconductor version 3.18 - BiocManager 1.30.23):
In
subsetGenes.xSeries
, when, for a given key value (e.g., gene symbol), more than one occurrence is found in the annotation table of the xSeries (i.e., the same duplicated SYMBOL for multiple ENSG IDs) no action is taken and each entry is assigned to a different bar in the final chart, even if its name is not unique. It should be better to provide a rule to collapse statistics of genes with the same key value (e.g., keeping only the most expressed or their sum...), provided that user's "subsetting intention" is based on geneset key, rather than on (unique) ENSG IDs...See the same problem in GOZER
The text was updated successfully, but these errors were encountered: