please help with "could not find function "ComBat.mc" "

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please help with "could not find function "ComBat.mc" "

Yuan Chun Ding

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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Re: please help with "could not find function "ComBat.mc" "

Jim Lemon-4
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 <[hidden email]> 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)
>
> ______________________________________________
> [hidden email] 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]]

______________________________________________
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Re: 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:[hidden email]]
Sent: Wednesday, November 11, 2020 5:36 PM
To: Yuan Chun Ding <[hidden email]>
Cc: [hidden email]
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 <[hidden email]<mailto:[hidden email]>> 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 rec
 eive 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)

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html<https://urldefense.com/v3/__http:/www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!7LIBMZ-Dl-TUctBxHgefJtTy8Nam0_pdDxu6OlxC4fddmXLyFrFFNuvLUbzY$>
and provide commented, minimal, self-contained, reproducible code.

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.