Question: Specifying wells in normalization for cellHTS2
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gravatar for Steve Taylor
11.9 years ago by
Steve Taylor100
Steve Taylor100 wrote:
Hi, I would like to specify normalization based on certain negative control wells using the package cellHTS2. I am trying: xn<-normalizePlates(x,scale="multiplicative",log=FALSE,method="negativ es",varianceAdjust="none",negControls=c("B12","C01","C12","D01","D12", "E01","F01")) but get: Error in checkControls(y = negControls, len = nrChannel, name = "negControls") : 'negControls' should be a vector of regular expressions with length 1 What's the best way to do this? Thanks for any help, Steve
normalization cellhts2 • 324 views
ADD COMMENTlink modified 11.9 years ago by ligia@ebi.ac.uk50 • written 11.9 years ago by Steve Taylor100
Answer: Specifying wells in normalization for cellHTS2
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gravatar for ligia@ebi.ac.uk
11.9 years ago by
ligia@ebi.ac.uk50 wrote:
Hi Steve, You have to specify the negative controls in a way that is consistent with how they were annotated by the plate configuration file. The default annotation for negative and positive controls is "neg" and "pos", respectively, and such annotation is assumed by "normalizePlates" when you choose to perform a controls-based normalization (i.e. you can omit the arguments negControls and/or posControls in this case, since they are by default set to posControls="pos" and negControls="neg"). Alternatively, you can use a more specific annotation for the controls in the plate configuration file, such as the name of the genes they target, etc., which is useful when you use different types of positive or negative controls. In this case, and as indicated in the help page of "normalizePlates", you can find an example on how to set the arguments "negControls" (and/or "posControls") in the help page of "summarizeChannels". I hope that I've answered your question. Cheers, Ligia > Hi, > > I would like to specify normalization based on certain negative control > wells using the package cellHTS2. I am trying: > > xn<-normalizePlates(x,scale="multiplicative",log=FALSE,method="negat ives",varianceAdjust="none",negControls=c("B12","C01","C12","D01","D12 ","E01","F01")) > > but get: > > Error in checkControls(y = negControls, len = nrChannel, name = > "negControls") : > 'negControls' should be a vector of regular expressions with length 1 > > What's the best way to do this? > > Thanks for any help, > > Steve > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 11.9 years ago by ligia@ebi.ac.uk50
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