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User: zicheng.hu

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zicheng.hu • 20
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Posts by zicheng.hu

<prev • 5 results • page 1 of 1 • next >
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How to find the degree of freedom, effect size and the variance of effect size for each contrast
... I have a treatment group and a control group. I calculated the "contrast' between them using functions in Limma: fit <- lmFit(array_data, design) cont.matrix <- makeContrasts(Effect ="treat-control", levels = design) fit2  <- contrasts.fit(fit, cont.matrix) fit2  <- eBayes(fit2)   I a ...
microarray limma written 11 months ago by zicheng.hu • 20 • updated 10 months ago by williamgeorge51547 • 0
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Comment: C: Error when reading the fcv file
... Thank you! It solves my problem.  ...
written 17 months ago by zicheng.hu • 20
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Comment: C: Error in the fsva function after setting "newdat" argument to NULL
... I ended up using the  removeBatchEffect function from limma.  SV = sva(expr,mod,mod0) expr = removeBatchEffect(x=expr, batch=NULL, batch2=NULL, covariates=SV$sv) ...
written 17 months ago by zicheng.hu • 20
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Error when reading the fcv file
... Dear flowCore maintainer,  I am developing a package that involves writing and reading fcs files.  I included an example in my package (modified here for simplicity) : library(flowCore) dat = as.matrix(iris[,1:4]) dat = flowFrame(dat) write.FCS(dat,"dat.fcs") dat = read.FCS("dat.fcs") I tested t ...
flowcore written 17 months ago by zicheng.hu • 20 • updated 17 months ago by Jiang, Mike • 1.2k
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Error in the fsva function after setting "newdat" argument to NULL
... I ran the example code from the sva page :  bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.R Everything works great. However, I got an error after I change the code in chunk 24 from  fsvaobj = fsva(trainData,trainMod,trainSv,testData) to  fsvaobj = fsva(trainData,trainMod, ...
sva written 20 months ago by zicheng.hu • 20 • updated 18 months ago by victor.2wy • 0

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