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User: zhang.jianhai

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Posts by zhang.jianhai

<prev • 44 results • page 1 of 5 • next >
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KEGGREST mapping between genes and pathways
... Hello, I want to enrich KEGG pathways on my rice genes. I tried "clusterProfiler", but its input is entrezID and my gene ids are RAPIDs (Os02g0617800). I want to keep using the RAPIDs, so I have to write my own enrichment functions. To do this, I need the mapping between RAPIDs and pathways. How to ...
keggrest mapping genes to pathways written 14 hours ago by zhang.jianhai0
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Comment: C: edgeR DEG glmQLFTest
... I got the answer from another post. It seems the replies cannot be deleted, so it is still here. ...
written 14 days ago by zhang.jianhai0
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Comment: C: edgeR DEG glmQLFTest
... I see. If I only test A-C, A-D using glmQLFTest, should I fit only A, C, D in glmQLFit, or fit all A-D then specify the coef as A-C, A-D in glmQLFTest? ...
written 14 days ago by zhang.jianhai0
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Comment: C: edgeR DEG glmQLFTest
... Now I understand. In the resulting table, can I filter out the genes by FDR and logFC at the same time? Or only by one of the two? ...
written 16 days ago by zhang.jianhai0
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Comment: C: edgeR DEG glmQLFTest
... If I only interested in 2 comparisons like A-C, A-D, one option is to use glmQLFTest to test all the 6 pairs, then extract A-C, A-D from the resulting table. Another option is to use glmQLFTest only test A-C, A-D. Which option is better? Regards, ...
written 16 days ago by zhang.jianhai0
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edgeR DEG glmQLFTest
... Hello, I have questions about the pvalues in the result from glmQLFTest. For example, I have 4 treatments A, B, C, D, each has 3 replicates, and I want to compare any treatment pairs, i.e.: A-B, A-C, A-D, B-C, B-D, C-D. I use a matrix, generated by "makeContrasts" to define all the contrasts, then ...
pvalue glmqlftest written 16 days ago by zhang.jianhai0 • updated 16 days ago by Gordon Smyth36k
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Comment: C: edgeR DEG how many treatments should be fitted to GLM
... Good answer. Thanks a lot! ...
written 25 days ago by zhang.jianhai0
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edgeR DEG how many treatments should be fitted to GLM
... Hello, I have questions about how many treatments should be fitted to GLM. Say, I have A, B, C, D 4 treatments, and 1 control, each treatment (including control) has 3 replicates. All treatments and control are the same species. I want to compare A against B and A against control. I am hesitating b ...
edger glm written 26 days ago by zhang.jianhai0 • updated 26 days ago by Gordon Smyth36k
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Comment: C: p.adjust function fdr and BH
... Hello Gordon, Now I understand. Thanks. Regards ...
written 7 months ago by zhang.jianhai0
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p.adjust function fdr and BH
... Hello, In the p.adjust R function, there are multiple adjust methods, as shown here: https://www.rdocumentation.org/packages/stats/versions/3.5.0/topics/p.adjust I read many posts, it seems the "BH" is used for "FDR", but why in the function "BH" and "fdr" are two independent methods? Another que ...
fdr bh written 7 months ago by zhang.jianhai0 • updated 7 months ago by Gordon Smyth36k

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Popular Question 7 months ago, created a question with more than 1,000 views. For Meaning of multiple coef in topTable, limma.

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