User: zhang.jianhai

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Posts by zhang.jianhai

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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 5 days ago by zhang.jianhai0
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Comment: C: T-test in limma
... Thank you very much, got it! Regards. ...
written 5 days 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 6 days 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 6 days ago by zhang.jianhai0 • updated 5 days ago by James W. MacDonald46k
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Comment: C: rice affymetrix qc() function
... Resolved. Thanks a lot. Regards ...
written 6 days 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 6 days 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 6 days ago by zhang.jianhai0 • updated 6 days ago by James W. MacDonald46k
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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 7 days ago by zhang.jianhai0 • updated 7 days ago by Gordon Smyth33k
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Can I ask questions on packages from CRAN?
... Hello, Can I ask questions on package heatmaply? (https://cran.r-project.org/web/packages/heatmaply/index.html) Regards ...
package from cran written 9 months ago by zhang.jianhai0 • updated 9 months ago by Valerie Obenchain ♦♦ 6.5k
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ggplot2 map color coded image with gene expression values.
... Hello, I am working on mapping gene expression data of microarray to color coded images. Specifically, the image is a line drawing of a plant with each organ coded with a unique color. The expression data correspond to different organs. I want to map these data to the corresponding organs. The desi ...
ggplot2 choropleth maps written 10 months ago by zhang.jianhai0

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