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Old 03-17-2015, 12:28 AM   #1
xunong
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Location: china

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Red face How do GO enrichment by GO-id?

Hi all,

Now I'm doing some analysis on Green algae which is not common species and exisiting software for GO is not applicable, so I wonder if it can be done by hypergeometric distribution in R?

I've got GO id for most of the 'genes'(not official gene names) and I found some 'genes' have more than one GO id, how do I edit my data file in this situation?And next, how to do hypergeometric distribution?

Can anyone help?

Thanks
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Old 03-17-2015, 07:18 AM   #2
reema
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Hello xunong

Hypergeometric distribution is used in case of microarray data.
Are you using RNAseq data? If yes- then i would suggest to use GOseq R package. You can create your own GO instance and then use it. Also use Wallenius approximation for RNA-seq data.
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Old 03-17-2015, 07:40 AM   #3
xunong
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Quote:
Originally Posted by reema View Post
Hello xunong

Hypergeometric distribution is used in case of microarray data.
Are you using RNAseq data? If yes- then i would suggest to use GOseq R package. You can create your own GO instance and then use it. Also use Wallenius approximation for RNA-seq data.
thank u reema,
yes, it is RNA-seq data, can't wait to try GOseq
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