Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Problem parsing some GSE matrices #45

Closed
grimbough opened this issue Nov 6, 2017 · 1 comment
Closed

Problem parsing some GSE matrices #45

grimbough opened this issue Nov 6, 2017 · 1 comment

Comments

@grimbough
Copy link

grimbough commented Nov 6, 2017

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.

@grimbough
Copy link
Author

After a bit more digging to find some example data where this was working as expected I've suggested a patch in #46

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant