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auerbachs / BMDExpress-3

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Annotation for zebrafish works with functional classification? #6

Open dageide opened 2 months ago

dageide commented 2 months ago

Hi, (thanks for a great application) Toxic model averaging works fine, as far as I can judge, but I never get any GO/reactome/bioplanet results for Danio rerio although mouse and fruitfly works fine (with orthologs from C elegans and D magna). I use danRer11_Ensembl annotation, get the entrezid correctly (checked NCBI), TMM normalised counts seem to work with ToxicR BMD. All tweaking with all settings in the GO/Reactome dialog result in the same: - "no columns in table". Run details below:

CLIP Gene Ontology Analyses

then, very often, BMDExpress 3.20 BUILD 0095 (MacOS 14.4.1, Intel) gets confused and lots of things go nuts. Must restart the app, reinstall app and annotation update doesn't help either.

thanks for advice, Dag

auerbachs commented 2 months ago

Sorry you are having issues. We have been have some challenges with the Mac version. In the expression data section when you right click your data file and select show annotations and select probe to genes do you see 3 column with data 1) Probe set ID, 2)Entrez genes and 3) Gene symbols? In the Entrez gene and Gene symbol columns are there values? Also what are the total number of rows in the table? If you are using Ensembl the probe set ID should look like this ...ENSDARG00000099961