[BioC] DWD method for batch effect removal

[Dan Tenenbaum]

On Wed, Aug 7, 2013 at 11:04 AM, Li Liu <liliu_1 at hotmail.com> wrote:
> HI,
>
> I am using inSilicoMerging package to remove batch effect. A few merging methods, such as  COMBAT, BMC, GENENORM, work well for me, so I suppose my dataset has no problem. However, when I use the method DWD, there is an error
> Error in is.factor(x) : object 'ybuf' not found
>  Is there anybody who can help this?
>

Seems like the problem is upstream in the DWD package. I've sent an
email with a bug report to the DWD maintainer. The problem seems
easily fixable. A workaround is to install an older version of DWD
from here:

http://cran.r-project.org/src/contrib/Archive/DWD/DWD_0.10.tar.gz

After downloading, you can install on the command line with
R CMD INSTALL DWD_0.10.tar.gz
or within R:

install.packages("DWD_0.10.tar.gz", repos=NULL, type="source")

Dan



> Thanks.
>
> Li
>
>
>
>> esets=list(eset1, eset2, eset3, eset4, eset5, eset6)
>
>> # Merge esets by different methods
>
>> library(inSilicoMerging)
> Loading required package: DWD
> Loading required package: Matrix
> Loading required package: lattice
>
>
>> eset_NONE=merge(esets, method='NONE')
>   INSILICOMERGING: Run NONE...
>
>> eset_BMC=merge(esets, method='BMC')
>   INSILICOMERGING: Run BMC...
>
>> eset_COMBAT=merge(esets, method='COMBAT')
>   INSILICOMERGING: Run COMBAT...
>   INSILICOMERGING:   => Found 6 batches
>   INSILICOMERGING:   => Found 0 covariate(s)
>
>> eset_GENENORM=merge(esets, method='GENENORM')
>   INSILICOMERGING: Run GENENORM...
>
>> eset_DWD=merge(esets, method='DWD')
>   INSILICOMERGING: Run DWD...
> Error in is.factor(x) : object 'ybuf' not found
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252
> [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Canada.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] inSilicoMerging_1.4.0 DWD_0.11              Matrix_1.0-12
> [4] lattice_0.20-15       hgu133acdf_2.12.0     AnnotationDbi_1.22.6
> [7] affy_1.38.1           Biobase_2.20.1        BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.28.0         BiocInstaller_1.10.3  DBI_0.2-7
>  [4] grid_3.0.1            IRanges_1.18.2        preprocessCore_1.22.0
>  [7] RSQLite_0.11.4        stats4_3.0.1          tools_3.0.1
> [10] zlibbioc_1.6.0
>
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>
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