Hi,
I am trying to run my microarray data through ComBat(in sva packge).Below
is my sampleinfo file.
When I run it with these commands

batch = sampleinfo$Batch
 mod = model.matrix(~as.factor(Covariate), data=sampleinfo)
combat_edata = ComBat(dat=edata, batch=batch, mod=mod, par.prior=TRUE,
prior.plots=FALSE)
I dont get any error and it runs with this message.
Found 10 batches
Found 3  categorical covariate(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data

But the problem is I have 4 covariate not three.

I even ran the example dataset in SVA package
 ## Load data
  library(bladderbatch)
  data(bladderdata)

  ## Obtain phenotypic data
  pheno = pData(bladderEset)
  edata = exprs(bladderEset)
  batch = pheno$batch
  mod = model.matrix(~as.factor(cancer), data=pheno)

  ## Correct for batch using ComBat
  combat_edata = ComBat(dat=edata, batch=batch, mod=mod, par.prior=TRUE,
prior.plots=FALSE)
This also give
Found 2  categorical covariate(s) when there are three covariates in this
dataset.


Please help,
Thank you,
Gayatri

 Array name Sample name Batch Covariate  C3D1 1 1 1  C3D2 2 1 1  C3D3 3 1 1
C3D5 4 2 1  C3D14 5 6 1  C3D15 6 6 1  C3D16 7 7 1  C3D17 8 7 1  C3D18 9 7 1
S3D7 10 3 2  S3D8 11 4 2  S3D9 12 4 2  S3D10 13 4 2  S3D11 14 5 2  S3D12 15
5 2  S3D19 16 8 2  S3D20 17 8 2  S3D21 18 9 2  S3D22 19 9 2  S3D23 20 10 2
S3D24 21 10 2  C25D1 22 1 3  C25D2 23 1 3  C25D3 24 2 3  C25D5 25 3 3
C25D14 26 6 3  C25D15 27 6 3  C25D16 28 7 3  C25D17 29 7 3  C25D18 30 8 3
S25D7 31 3 4  S25D8 32 4 4  S25D9 33 4 4  S25D10 34 5 4  S25D11 35 5 4
S25D12 36 5 4  S25D19 37 8 4  S25D21 38 9 4

S25D23
39 10

4

	[[alternative HTML version deleted]]

