Error on "Estimation of cluster number" in VSCLust

GTPB / IBIP19

IBIP19 - Integrative Biological Interpretation using Proteomics (2019)

https://gtpb.github.io/IBIP19/

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Error on "Estimation of cluster number" in VSCLust #4

Closed iquasere closed 4 years ago

iquasere commented 4 years ago

Greetings again! This question goes to Veit!

I want to know what parameters I should set when inputing the "PMC6453966_VSClust_in.csv" file for VSClust. I have set:

Yes for: "Column names?", "Estimate variance levels from replicated quantifications?" and "Replicates are grouped"
No for: "Gene/protein identifiers in second column?" and "paired tests"
Number of replicates: 9
Number of conditions: 5

With this parameters, when I try to do "Estimation of cluster number", I get

Error: non-numeric argument to binary operator

veitveit commented 4 years ago

I think you have the wrong file. I went through the notebook, created it and loaded it into VSClust without problems https://drive.google.com/open?id=1VdZSPfT6KSmyBI_svmUP_u2yn4QrJNko Can you check whether this file works with you?

You might have chosen the wrong columns when creating the file

iquasere commented 4 years ago

Of course you were right, I had selected the "PSMs.for.quant" columns. It works perfectly for estimating cluster number. Now I run into the problem of enrichment. I am using the server version of the software, no docker. When I try to "run enrichment", with ID type as "UNIGENE" and Information resource as "GO molecular function" or any other, it fails. "A1BG", the first rowname, is a UniProt gene name, but I also tried setting the ID type for other values and always gives me

No result. Wrong ID type?

At least the next people will know how to not follow my mistakes xD

veitveit commented 4 years ago

Good point. The correct term would be "OFFICIAL_GENE_SYMBOL", but the used R library (RDAVIDWebservice) does not seem capable of using this indentifier.

You could upload the file that has been prepared for ComplexBrowser as it contains UniProt accession numbers instead. I probably will have to move this conversion to an earlier stage.