## User: s.apocarpum

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#### Posts by s.apocarpum

<prev • 12 results • page 1 of 2 • next >
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... Hi, Recently i've posted a couple of comments on Biostars web site: "Why we need to make a GLM model before performing a Wald test itself (as i can understand it's just a simple t-test in rough approximation?)? Why not just perform a Wald test on count data?" "In addition, when i perform ...
written 5 weeks ago by s.apocarpum0 • updated 5 weeks ago by wunderl20
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... Yes, of course, i've read the mentioned above section and even posted a couple of related questions a while ago (https://support.bioconductor.org/p/71326/#71391 and https://support.bioconductor.org/p/71069/). Since that time, for me was clear that genes without GO annotation at all are invisible for ...
written 3.8 years ago by s.apocarpum0
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... Hi, thanks for your response! From your example i can guess you deal with some DE experiment data and model organism. But both are not the case for me. Please check the "4.3 Custom annotations" and "4.4 Predefined list of interesting genes" sections of topGO manual. That's what i do. I checked the t ...
written 3.8 years ago by s.apocarpum0
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... I'm going to perform GO enrichment test on my data set with topGO package. But i have some number of obsolete GO terms both in my gene universe and the list of genes of interest. Will they are just invisible for the software or they will somehow contribute to the analysis?  ...
written 3.8 years ago by s.apocarpum0
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... I have list of genes with GO labels. Some of the GOs are quite general, others very specific. I believe it could influence on GO enrichment analysis that i'm going to conduct on those gene list. Now i'm looking for a way to normalize my GOs so that after normalization i could get the same gene list, ...
written 3.8 years ago by s.apocarpum0 • updated 2.3 years ago by Lluís Revilla Sancho500
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... I have a gene universe and list of genes of interest. Both are annotated with GO labels. But some of the GOs a very specific, another ones, contrary, are very broad. Could this fact introduce some bias in my GO enrichment analysis (with topGO package) ? Whether will be GO enrichment analysis on GO s ...
written 3.8 years ago by s.apocarpum0
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... Thank you so much! It's a really excellent explanation!!! ...
written 3.9 years ago by s.apocarpum0
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... There is a code example in the "Performing the test" chapter of the topGO manual: >test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher test") >resultFisher <- getSigGroups(GOdata, test.stat) > resultFisher   Description: GO analysis of ALL data; B-cel ...
written 3.9 years ago by s.apocarpum0 • updated 3.9 years ago by James W. MacDonald50k
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... I've checked my topGOdata objects. The reason was a presence of additional "\" characters in the created objects. So, problem appeared because of bad formatting of input data. Now the amount of feasible genes corresponds to number of genes with GO annotation in my data. ...
written 3.9 years ago by s.apocarpum0
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... I have 34727 genes in my gene universe. From those only 19622 have at least one GO term attached. Also there is  list of genes of interest with 467 genes, out of them only 80 have GO annotation. From those data i created three topGOdata objects: one for terms related to biological process, another o ...
written 3.9 years ago by s.apocarpum0

#### Latest awards to s.apocarpum

Popular Question 3.8 years ago, created a question with more than 1,000 views. For What is Nontrivial node in topGO analysis?

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