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

[Jim Lemon]

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> 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
>
> ----------------------------------------------------------------------
> ------------------------------------------------------------
> -SECURITY/CONFIDENTIALITY WARNING-
>
> This message and any attachments are intended solely for the individual or
> entity to which they are addressed. This communication may contain
> information that is privileged, confidential, or exempt from disclosure
> under applicable law (e.g., personal health information, research data,
> financial information). Because this e-mail has been sent without
> encryption, individuals other than the intended recipient may be able to
> view the information, forward it to others or tamper with the information
> without the knowledge or consent of the sender. If you are not the intended
> recipient, or the employee or person responsible for delivering the message
> to the intended recipient, any dissemination, distribution or copying of
> the communication is strictly prohibited. If you received the communication
> in error, please notify the sender immediately by replying to this message
> and deleting the message and any accompanying files from your system. If,
> due to the security risks, you do not wish to receive further
> communications via e-mail, please reply to this message and inform the
> sender that you do not wish to receive further e-mail from the sender.
> (LCP301)
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

	[[alternative HTML version deleted]]