How do GO enrichment by GO-id？

xunong · 03-17-2015, 12:28 AM

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

reema · 03-17-2015, 07:18 AM

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.

xunong · 03-17-2015, 07:40 AM

Quote:

Originally Posted by reema

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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03-17-2015, 12:28 AM	#1
xunong Junior Member Location: china Join Date: Sep 2014 Posts: 9	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

03-17-2015, 07:18 AM	#2
reema Member Location: Scotland Join Date: Feb 2014 Posts: 27	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.