User: zicheng.hu
zicheng.hu • 20
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Posts by zicheng.hu
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3
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... 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 ...
written 13 months ago by
zicheng.hu • 20
• updated
12 months ago by
williamgeorge51547 • 0
0
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1
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385
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1
answers
Comment:
C: Error when reading the fcv file
... Thank you! It solves my problem.
...
written 19 months ago by
zicheng.hu • 20
0
votes
1
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349
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1
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... 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 19 months ago by
zicheng.hu • 20
0
votes
1
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385
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1
answer
... 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 ...
written 19 months ago by
zicheng.hu • 20
• updated
19 months ago by
Jiang, Mike • 1.2k
2
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1
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349
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1
answer
... 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, ...
written 22 months ago by
zicheng.hu • 20
• updated
20 months ago by
victor.2wy • 0
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