[BioC] ComBat

[Valerie Obenchain]

Hi Gayatri,

Following the example on the ComBat man page as you have done, I see 2 
covariates, not 3.

The model matrix shows 'cancer' and 'normal' covariates:

> head(mod)
              (Intercept) as.factor(cancer)Cancer as.factor(cancer)Normal
GSM71019.CEL           1                       0                       1
GSM71020.CEL           1                       0                       1
...
...

The intercept is not considered a categorical covariate.

I've cc'd the package authors in case they have something else to add.

Valerie


On 01/03/2013 01:31 PM, Gayatri Iyer wrote:
> 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]]
>
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