[BioC] first time using combat

[Johnson, William Evan]

Fernando, 

Capitalize the "b" in the "Batch" header, and let me know if this works. Alternatively, use the ComBat from the sva package of bioconductor. This will be less finicky.

Evan


On Jun 4, 2013, at 11:12 AM, Fernando Andrade wrote:

> Hi there,
> 
> This is the first time using combat, and i'm using it on a very large set of data built up in 14 batches. I'm gettin many error messages when running it, and i've searched for every single one of them in ComBat forum and tried to fix using the information available in the forum, but i'm still getting errors. Every time that I use tab-separeted values i get an error saying that a I have non numerical values, then i move to .csv ant the error changes:
> 
> Reading Sample Information File
> Reading Expression Data File
> Found 0 batches
> Found 0 covariate(s)
> Standardizing Data across genes
> Error in solve.default(t(design) %*% design) : 
>   Lapack routine dgesv: system is exactly singular: U[1,1] = 0
> 
> or
> 
> Reading Sample Information File
> Reading Expression Data File
> Found 0 batches
> Found 5 covariate(s)
> Error in matrix(0, length(vec), nlevels(vec) - start + 1) : 
>   invalid 'ncol' value (< 0)
> 
> my expression file is formatted like this:
> 
> probe       lineage1       lineage2       lineage3...
> xxx          11.111         22.2222        333.3333 ....
> ...
> 
> and my sif is like this:
> 
> ID          batch
> lineage1     1
> lineage2     1
> lineage3     2
> lineage4     3...
> 
> I'd be very grateful for any help!
> thanks for your attention
> 
> Fernando