How to do goseq with user created "lengthData" and category mapping objects?

1

Entering edit mode

10.2 years ago

Parham ★ 1.6k

Hi,

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 this post. 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.

Thanks!

gene.vector lengthdata goseq category-mapping • 3.5k views

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by Parham ★ 1.6k

1

Entering edit mode

Hi!

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

Thanks!

ADD REPLY • link updated 2.9 years ago by Ram 44k • written 10.1 years ago by beanavarro85 ▴ 10

0

Entering edit mode

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

ADD REPLY • link 10.1 years ago by Parham ★ 1.6k

0

Entering edit mode

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 REPLY • link 8.4 years ago by jimreaper1066 • 0

Login before adding your answer.