User: s.apocarpum

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Posts by s.apocarpum

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DESeq2 GLM modelling and Wald's test
... 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 ...
deseq2 written 5 weeks ago by s.apocarpum0 • updated 5 weeks ago by wunderl20
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Comment: C: Obsolete GO terms in topGO analysis
... 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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Comment: C: Obsolete GO terms in topGO analysis
... 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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Obsolete GO terms in topGO analysis
... 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?  ...
topgo written 3.8 years ago by s.apocarpum0
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Normalization of specificity level (level of depth) of GO terms dataset
... 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, ...
gosemsim gosim written 3.8 years ago by s.apocarpum0 • updated 2.3 years ago by Lluís Revilla Sancho500
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GO enrichment analysis Vs GO slims enrichment analysis
... 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 ...
topgo written 3.8 years ago by s.apocarpum0
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Comment: C: What is Nontrivial node in topGO analysis?
... Thank you so much! It's a really excellent explanation!!! ...
written 3.9 years ago by s.apocarpum0
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What is Nontrivial node in topGO analysis?
... 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 ...
topgo written 3.9 years ago by s.apocarpum0 • updated 3.9 years ago by James W. MacDonald50k
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Answer: A: Understanding of "feasible genes" conception
... 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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Understanding of "feasible genes" conception
... 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 ...
topgo written 3.9 years ago by s.apocarpum0

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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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