Example file in GUI format doesn't work

[maxkfranz]

Describe the bug
A clear and concise description of what the bug is.

Using the GSE129943_rsem_counts_2016 example file, but formatted like the UI says doesn't work.

To Reproduce
Steps to reproduce the behavior:

1. Download the file I've attached. It just has a Gene column with the names, like the UI says. No Ensembl.
2. Try it.
3. The UI errors out.

GSE129943_rsem_counts_2016.csv

It doesn't work as tab-delimited either:
GSE129943_rsem_counts_2016.txt

Expected behavior
A clear and concise description of what you expected to happen.

The file should go through. Not everyone will have Ensembl.

Screenshots
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Desktop (please complete the following information):

• OS: Mac 14.3.1
• Browser Safari
• Version 17.3.1

It doesn't work in Chrome either.

[mikekucera]

There are several rows where the gene name is missing. There are also several rows where the gene name is "NA".

This causes an error from FGSEA.

<simpleError in data.frame(logFC = logFC, logCPM = glmfit$AveLogCPM, LR = LR, PValue = LRT.pvalue, row.names = rn): row names contain missing values>

[mikekucera]

We can add validation logic on the client to check for cases like this, and provide better error messages. But in this case if the user had opened their file in any editor they should be able to see the obvious formatting errors. I don't think automatically filtering out the bad rows is a good idea, the user should know that there's problems with their data.

What do you guys think?

[maxkfranz]

There are way too many rows in real data to just scroll through it in Excel. People give up and "the site is broken".