User: Iain Wallace

gravatar for Iain Wallace
Iain Wallace50
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50
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New User
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Last seen:
10 years, 4 months ago
Joined:
10 years, 5 months ago
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i*************@gmail.com

Posts by Iain Wallace

<prev • 5 results • page 1 of 1 • next >
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Gostats and custom list
... Hi Marc, I just wanted to let you know that I found a bioconductor package, PCPheno, (link ) that allows me to use use HyperGTest with custom lists. All I have to turn the list of categories in to a binary matrix, where my rows are my genes, and the columns are the different categories and the entr ...
annotation pathways go yeast convert gostats category written 10.4 years ago by Iain Wallace50
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Comment: C: Gostats and custom list
... Hi Marc, Thanks for getting back to me. I did read the GOstats vignette, but I wasn't clear how to define a new set of categories. I have no idea how to define a new subclass, as suggested by HyperGtest man page which says "To add support for a new FOO category type, a developer would need to creat ...
written 10.4 years ago by Iain Wallace50
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Gostats and custom list
... Hi all, I was wondering if anybody could give me pointers on how to use GOstats with a custom list of gene annotations/categories I have my list of yeast genes associated with one or more of 25 different categories My file looks something like this: Gene_A Category_1 Gene_A Category_2 Gene_B Cate ...
annotation yeast convert gostats annotationdbi written 10.4 years ago by Iain Wallace50 • updated 10.4 years ago by Marc Carlson7.2k
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Comment: C: How to use GOSlim with GOstats
... Hi Marc, I am trying to summarize the GO results for lots of experiments. GOslim was recommended to me as it gives a nice overview. Ideally I would like to have a vector for each experiment, showing a score for each GOslim term which I can then colour/cluster based on over representation I am not ...
written 10.4 years ago by Iain Wallace50
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How to use GOSlim with GOstats
... Hi all, I was wondering if somebody could point me in the right direction. I would like to use GOSlim from the SGD websitewith the GOStats package, but I am not sure how to change the ontology/annotation. I am currently using the following set of commands to do my Go analysis. library(GOstats) lib ...
gostats written 10.4 years ago by Iain Wallace50 • updated 10.4 years ago by Marc Carlson7.2k

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