PCA plot and sample correlation error

[alyssaxin]

Hello,

I've ran an LFQ experiment and gotten the resulting combined_protein.tsv, however no experiment annotation file was generated. Nonetheless, I've made my own experiment annotation tsv file and inputted this into FragPipe Analyst. I managed to get the significant proteins, volcano plots and other results, but could not get the PCA plot and sample correlation results. The error message appeared: An error has occurred. Check your logs or contact the app author for clarification.

Can I ask for advice on how to get the PCA plot and sample correlation plot?

Cheers, Alyssa

[hsiaoyi0504]

@alyssaxin Is this duplicated with the last one you submitted? #79 Would you mind sharing the file with me? yihsiao@umich.edu. It's not really possible to know what's the issue based on what you described.

[hsiaoyi0504]

Just for future reference. It looks like the data submitted don't have any non-missing values in the intensity columns. It might be because users not correctly configured FragPipe and performed the search.

[hsiaoyi0504]

Closed as solved.