[BioC] DWD method for batch effect removal

[Dan Tenenbaum]

On Wed, Aug 7, 2013 at 11:37 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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?
>>

I've checked version 1.4.1 of inSilicoMerging which contains a
workaround for this problem.
It will be available tomorrow around 10:30AM Seattle time (or now via
svn). Devel version has been fixed as well.

Thanks,
Dan



>
> 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
>>
>>         [[alternative HTML version deleted]]
>>
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