Empty space in the Samples input file causes an error message

[AxelBigOmics]

This is something that can be fixed manually, but Ivo suggested adding a check to remove it. Whenever I leave an empty space before or after a phenotype descriptor (see attached figure), the platform complains that there are no samples for a given phenotype.

I guess this could be solved informatically by removing empty spaces before/after the phenotype description.

[stefanreifenberg]

We could simply trim whitespaces in the upload process. I can look into this once I am done with the current issues.

[AxelBigOmics]

Sounds good. Thanks for the prompt reply, Stefan!

[stefanreifenberg]

Could you please provide me an example file with the whitespace error to reproduce the issue

[AxelBigOmics]

Sure thing. Here are the original red counts file and the samples file with the spaces.

counts.csv samples_error.csv

[stefanreifenberg]

I used these files and did not get an error so far. What do I have to do to reproduce the error described above?

[AxelBigOmics]

You should try to create pairwise comparisons using the "Contrasts" tab with either the "Gender" or "Disease" phenotypes. That is where an error shows up.

[stefanreifenberg]

Ok, can you also please send me the contrasts.csv file?

[AxelBigOmics]

I would, except I normally generate it through the platform and because of the error message, I cannot create a contrast.csv file with the platform. I've included the actual error message below.

[ivokwee]

@stefanreifenberg is this done? As you said, after loading CSV we can use trimws().

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This issue was closed because it has been inactive for 14 days since being marked as stale.