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Question: Error in the fsva function after setting "newdat" argument to NULL
2
gravatar for zicheng.hu
20 months ago by
zicheng.hu20
zicheng.hu20 wrote:

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,trainSv,newdat=NULL)

Error message: Error in fsva(trainData, trainMod, trainSv, newdat = NULL) : object 'newV' not found

Why am I not allowed to set "newdat" argument to NULL here?  I want to clean the data using sva for clustering and PCA analysis, so I don't have test data. Can I only adjust the training data using fsva?

sva • 331 views
ADD COMMENTlink modified 18 months ago by victor.2wy0 • written 20 months ago by zicheng.hu20
Answer: Error in the fsva function after setting "newdat" argument to NULL
0
gravatar for victor.2wy
18 months ago by
victor.2wy0
victor.2wy0 wrote:

Did you ever figure this out?

I'm running into the same error.

ADD COMMENTlink written 18 months ago by victor.2wy0

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)

ADD REPLYlink written 17 months ago by zicheng.hu20
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