[BioC] ComBat() -- run with one sample in one batch

Guest [guest] guest at bioconductor.org
Fri Jun 6 20:43:49 CEST 2014


Is there a work around for ComBat() where I can run the function if I have only one sample in one batch?

I'm working with affymetrix, human chip U133A and trying to remove batch effect on scan date. I have some samples that were scanned individually on separate dates. So there are some dates where only one sample was run.

Any insight regarding this will be appreciated.


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bladderbatch_1.2.0   sva_3.10.0           mgcv_1.7-29          nlme_3.1-117         corpcor_1.6.6        affy_1.42.2         
[7] Biobase_2.24.0       BiocGenerics_0.10.0  BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] affyio_1.32.0         grid_3.1.0            lattice_0.20-29       Matrix_1.1-3          preprocessCore_1.26.1
[6] tools_3.1.0           zlibbioc_1.10.0      

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