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6.8 years ago
I was wondering if there is a way to obtain list of enriched processes and pathways using goseq by providing only list of significant ensembl geneid or symbols for mm9, has any one tried this if yes can could you please share code snippet or steps on how to go about this?
Thank you
That would kind of eliminate the point of goseq.
True, still curious any work around? reason i need to do this is i am trying to determine enrichment of genes with dysregulated junctions from mats output, with goseq you need provide list of genes (unique) whereas in my case i could have two significant junction that belong to same gene/id not sure if i can input duplicate geneids in goseq
You could fake the normal inputs, but again at that point you should just use something else.
Could you plz explain with an example what you mean by fake input?
Look at what goseq needs as input. Compare that to what you have. Make up constant numbers for the rest. I won't give you an example of this, it's a nonsensical exercise.