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The refactored code for parsing GSE matrices seems to fail in some cases e.g. GSE5350 which we use in the BeadArrayUseCases vignette.
A straightforward path to producing the error is to try calling parseGSEMatrix on the GEO series text file directly:
GEOquery:::parseGSEMatrix(fname = "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5350/matrix/GSE5350-GPL2507_series_matrix.txt.gz")`
Error in enc2utf8(col_names(col_labels, sep = sep)) :
argument is not a character vector`
Some rudimentry digging leads me to think this is an issue with how the Sample_characteristics_ch1 field is being processed, but I don't know enough about how that may look across multiple datasets to offer a generic solution.
Happy to do some more experimentation if needed.
The text was updated successfully, but these errors were encountered:
The refactored code for parsing GSE matrices seems to fail in some cases e.g. GSE5350 which we use in the BeadArrayUseCases vignette.
A straightforward path to producing the error is to try calling
parseGSEMatrix
on the GEO series text file directly:Some rudimentry digging leads me to think this is an issue with how the Sample_characteristics_ch1 field is being processed, but I don't know enough about how that may look across multiple datasets to offer a generic solution.
Happy to do some more experimentation if needed.
The text was updated successfully, but these errors were encountered: