Question: Error in the fsva function after setting "newdat" argument to NULL
2
gravatar for zicheng.hu
2.4 years ago by
zicheng.hu • 20
zicheng.hu • 20 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 • 406 views
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modified 2.2 years ago by victor.2wy • 0 • written 2.4 years ago by zicheng.hu • 20
Answer: Error in the fsva function after setting "newdat" argument to NULL
0
gravatar for victor.2wy
2.2 years ago by
victor.2wy • 0
victor.2wy • 0 wrote:

Did you ever figure this out?

I'm running into the same error.
ADD COMMENT • link written 2.2 years ago by victor.2wy • 0

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 REPLY • link written 2.1 years ago by zicheng.hu • 20
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