User: zhang.jianhai

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Posts by zhang.jianhai

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Comment: C: p.adjust function fdr and BH
... Hello Gordon, Now I understand. Thanks. Regards ...
written 11 weeks 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 11 weeks ago by zhang.jianhai0 • updated 11 weeks ago by Gordon Smyth35k
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Comment: C: rice annotation package
... That's very useful. How can I get all the host names? It seems there is not listHosts() function. Regards. ...
written 4 months ago by zhang.jianhai0
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Comment: C: T-test in limma
... Thank you very much, got it! Regards. ...
written 4 months ago by zhang.jianhai0
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Comment: C: T-test in limma
... If it does not work like I said, is the DEG calculation process in limma/edgeR essentially based on t-test/F-test? If not, what test is the foundation? Regards. ...
written 4 months ago by zhang.jianhai0
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rice annotation package
... Hello, Is there an equivalent package for rice Affymetrix like Arabidopsis (https://bioconductor.org/packages/release/data/annotation/html/ath1121501.db.html)? I want to retrieve the annotations by using rice affymetrix ids. Regards, Jianhai ...
rice annotation package written 4 months ago by zhang.jianhai0 • updated 4 months ago by James W. MacDonald47k
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Comment: C: rice affymetrix qc() function
... Resolved. Thanks a lot. Regards ...
written 4 months ago by zhang.jianhai0
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Comment: C: rice affymetrix qc() function
... Hello, I tried this, but still gives error. > cdfName(gse4471)                                                                           [1] "Rice" > qc4471 <- qc(gse4471, mas4471, cdfn="Rice")                                                Error in setQCEnvironment(cdfn) :    Could not fi ...
written 4 months ago by zhang.jianhai0
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rice affymetrix qc() function
... Hello, When I process a rice GEO file (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4471), it gives the following errors. Anyone know how to solve it? library(affy); library(simpleaffy); library(affyPLM); library(ricecdf) gse4471 <- ReadAffy(celfile.path=paste0("GSE4471", "_RAW")) m ...
affymetrix qc written 4 months ago by zhang.jianhai0 • updated 4 months ago by James W. MacDonald47k
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T-test in limma
... Dear all, I am confused about how t-test or F-test is implemented in limma/edgeR. Let's say I have a small dataset: two conditions, each condition has 3 replicates, and there are 4 genes. Con1 rep1 Con1 rep2 Con1 rep3 Con2 rep1 Con2 rep2 Con2 rep3 gene1     ...
limma t test written 4 months ago by zhang.jianhai0 • updated 4 months ago by Gordon Smyth35k

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