[R] please help with "could not find function "ComBat.mc" "

[Yuan Chun Ding]

Hi Jim,

Thank you for the message!  Yes, you are right, I contacted Dr. Xu Zongli,  he said he removed the ComBat.mc function from the new version.

Ding

From: Jim Lemon [mailto:drjimlemon using gmail.com]
Sent: Wednesday, November 11, 2020 5:36 PM
To: Yuan Chun Ding <ycding using coh.org>
Cc: r-help using r-project.org
Subject: Re: [R] please help with "could not find function "ComBat.mc" "

Hi Yuan,
The package named "Enmix" is maintained on Bioconductor. It seems to be specific to particular lab equipment and so all I can advise is:

1) Try your question on the Bioconductor help list
2) If no help there contact Zongli Xu (the maintainer)

Jim

On Thu, Nov 12, 2020 at 11:40 AM Yuan Chun Ding <ycding using coh.org<mailto:ycding using coh.org>> wrote:

Hi All,

I am very sorry to bother you.

This week, I updated my R from 3.5.3  to 4.0.3, reinstalled all required R packages  and reran the following R code;  then got the following error: could not find function "ComBat.mc".

> #' firstly Removing chip-well batch effects using ComBat from the sva package
> # First we convert from beta-values to M-values
> Mvals1 <- log2(betas.rcp)-log2(1-betas.rcp)
> #' ComBat eBayes adjustment using a known variable of interest (here we use row)
> Mvals.ComBat1 <- ComBat.mc(Mvals1, batch = pData(WB.noob)$Array,nCores = detectCores()-1)
Error in ComBat.mc(Mvals1, batch = pData(WB.noob)$Array, nCores = detectCores() -  :
  could not find function "ComBat.mc"

I have successfully run the same R code with same data sets several times since 2017.  Google searching tells me that this ComBat.mc function is from an R package "Enmix".  When typing library(Enmix), no error message, so the Enmix library is installed.  Can you tell me why I got this error after updating to new R version?

Thank you,

Yuan Chun Ding

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