Question: How to do goseq with user created "lenghtData" and category mapping objects?
gravatar for Parham
5.6 years ago by
Parham1.4k wrote:


I am doing goseq for S. pombe but since the organism is not on the database I had to create the lengthData from biomart. Then for category mapping I couldn't figure out the parameters for "makeOrgPackageFromNCBI", see makeOrgPackageFromNCBI for S. pombe. Finally I thought to download the GO category from Gene Ontology website from this link and I have to add that I have my DE genes calculated with DESeq2 already and I created the gene.vector from that also. 

My problem is the goseq manual only shows the standard workflow. I mean using edgeR and the information on the database for gene lengths and GO categories and doesn't show how to use the above mentioned user created objects! Or at least it is not very clear to me how to do it. I am no bioinformaticians so its hard for me to figure out things like this if there is a twist in them. If anyone can help me in this I truly appreciate that. Let me know if you want more information. 


ADD COMMENTlink modified 5.5 years ago by beanavarro850 • written 5.6 years ago by Parham1.4k
gravatar for beanavarro85
5.5 years ago by
European Union
beanavarro850 wrote:


I have the same problem here, did you get any answers or find a solution?


ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by beanavarro850

I solved it but not by makeOrgPackageFromNCBI. What organism do you work on?

ADD REPLYlink written 5.5 years ago by Parham1.4k

Mind sharing your solution? I am working with a bacterium, and have no idea how to format or import my GO mappings from blast2go.

ADD REPLYlink written 3.8 years ago by jimreaper10660
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