User: zhang.jianhai

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Posts by zhang.jianhai

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Normalisation upstream rlog
... Can you share the link of the workflow that contains the transformation section? Regards. ...
written 19 days ago by zhang.jianhai0
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Normalisation upstream rlog
... Hello, In the RNA Seq count data, upstream rlog normalisation should there be other normalisations like RPKM, CPM, etc.? Or the rlog is directly applied on raw count data? Regards. ...
deseq2 rlog written 20 days ago by zhang.jianhai0 • updated 20 days ago by Michael Love23k
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Comment: C: KEGGREST mapping between genes and pathways
... I am working on locus IDs, to convert transcript ids to locus ids, should I replace "t" with "g" (based on your link, it seems yes)? ...
written 8 weeks ago by zhang.jianhai0
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clusterProfiler GeneRatio minGSSize
... Hello, I am using "enrichKEGG" on rice genes. The entriz ids are `entr <- c("4337100", "4336350", "4324731", "4336393", "4347034", "4345789", "4336561", "107276072", "4324047", "4352785", "4344600", "4327916", "4328844", "4336915", "4338072", "4339251", "4325336", " ...
enrichkegg generatio written 8 weeks ago by zhang.jianhai0
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Comment: C: KEGGREST mapping between genes and pathways
... All the gene ids have a "t" (Os01t0118000) inside rather than a "g" (Os05g0532600). Why is that? ...
written 8 weeks ago by zhang.jianhai0
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Comment: C: KEGGREST mapping between genes and pathways
... I see. Thank you very much for reply! ...
written 9 weeks ago by zhang.jianhai0
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Comment: C: KEGGREST mapping between genes and pathways
... It is very useful, but why there is "-01" or "-00" at the end of gene IDs (e.g. Os01t0191700-01)? ...
written 9 weeks ago by zhang.jianhai0
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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 9 weeks ago by zhang.jianhai0 • updated 9 weeks ago by Gordon Smyth37k
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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 11 weeks 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 11 weeks ago by zhang.jianhai0

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Popular Question 9 months ago, created a question with more than 1,000 views. For Meaning of multiple coef in topTable, limma.

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