FlowCore: transform() NAs introduced by coercion
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@allenby-mark-6637
Last seen 7.3 years ago
All, I have been trying to transform my data by logicle and inverse logicle transformations. However, even when I copy the logicle transformation parameters the software estimates, the transform function still does not work, and brings up the warning NAs introduced by coercion. I am wondering if I am defining my inputs in improper form? Could anyone help me out? An example is below: ------------------ samp <- read.FCSfile.name, transformation=FALSE) lgcl <- estimateLogicle(samp, logchannels) x <- transform(x,lgcl) Wset <- as.list(environment(lgcl at transforms "488-530/30-A"@f))$w Tset <- as.list(environment(lgcl at transforms "488-530/30-A"@f))$t Mset <- as.list(environment(lgcl at transforms "488-530/30-A"@f))$m Aset <- as.list(environment(lgcl at transforms "488-530/30-A"@f))$a logicle <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset, 'logicle') invLgcl <- inverseLogicleTransform(trans = logicle) samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A")) ---------------------- The final line produces the warning: 1: In invLgcl("488-530/30-A") : NAs introduced by coercion Would anyone have an idea about what I might be doing incorrectly? I am new to R and flowCore, so it could be a basic problem I am overlooking. Thank you all so much for your help. Sincerely, Mark PhD at ICL -----Original Message----- From: Allenby, Mark Sent: 10 July 2014 16:11 To: bioconductor at r-project.org Subject: FlowCore: Extracting parameters from estimateLogicle All, Is there a way to extract the A, T, M, W logicle parameters from the estimateLogicle function? i.e. lgcl <- estimateLogicle(samp, logchannels) and extract parameters estimated from lgcl. Mark
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Greg Finak ▴ 240
@greg-finak-4299
Last seen 4.9 years ago
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You're trying to inverse transform your raw data rather than your transformed data, which is x, not samp. On Thu, Jul 10, 2014 at 11:14 AM, Allenby, Mark <mark.allenby@imperial.ac.uk> wrote: > All, > > I have been trying to transform my data by logicle and inverse logicle > transformations. However, even when I copy the logicle transformation > parameters the software estimates, the transform function still does not > work, and brings up the warning NAs introduced by coercion. I am wondering > if I am defining my inputs in improper form? Could anyone help me out? An > example is below: > > ------------------ > > samp <- read.FCSfile.name, transformation=FALSE) > lgcl <- estimateLogicle(samp, logchannels) > x <- transform(x,lgcl) > > Wset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$w > Tset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$t > Mset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$m > Aset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$a > > logicle <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset, > 'logicle') > invLgcl <- inverseLogicleTransform(trans = logicle) > samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A")) > > ---------------------- > > The final line produces the warning: > > 1: In invLgcl("488-530/30-A") : NAs introduced by coercion > > Would anyone have an idea about what I might be doing incorrectly? I am > new to R and flowCore, so it could be a basic problem I am overlooking. > Thank you all so much for your help. > > Sincerely, > > Mark > PhD at ICL > > -----Original Message----- > From: Allenby, Mark > Sent: 10 July 2014 16:11 > To: bioconductor@r-project.org > Subject: FlowCore: Extracting parameters from estimateLogicle > > All, > > Is there a way to extract the A, T, M, W logicle parameters from the > estimateLogicle function? > > i.e. lgcl <- estimateLogicle(samp, logchannels) and extract parameters > estimated from lgcl. > > Mark > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109 (206)667-3116 gfinak@fhcrc.org [[alternative HTML version deleted]]
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@allenby-mark-6637
Last seen 7.3 years ago
--------Sorry for double-posting, I didn't space my code properly------------ All, I have been trying to transform my data by logicle and inverse logicle transformations. However, even when I copy the logicle transformation parameters the software estimates, the transform function still does not work, and brings up the warning NAs introduced by coercion. I am wondering if I am defining my inputs in improper form? Could anyone help me out? An example is below: ------------------ samp <- read.FCSfile.name, transformation=FALSE) lgcl <- estimateLogicle(samp, logchannels) x <- transform(x,lgcl) Wset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$w Tset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$t Mset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$m Aset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$a logicle <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset, 'logicle') invLgcl <- inverseLogicleTransform(trans = logicle) samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A")) ---------------------- The final line produces the warning: 1: In invLgcl("488-530/30-A") : NAs introduced by coercion Would anyone have an idea about what I might be doing incorrectly? I am new to R and flowCore, so it could be a basic problem I am overlooking. Thank you all so much for your help. Sincerely, Mark PhD at ICL [[alternative HTML version deleted]]
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
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It can be fixed by using back tics instead of quote marks. i.e. samp <- transform(x, `488-530/30-A` = invLgcl(`488-530/30-A`)) On 07/11/2014 03:00 AM, bioconductor-request@r-project.org wrote: > Subject: > [BioC] FlowCore: transform() NAs introduced by coercion > From: > "Allenby, Mark" <mark.allenby@imperial.ac.uk> > Date: > 07/10/2014 11:14 AM > > To: > "bioconductor@r-project.org" <bioconductor@r-project.org> > > > All, > > I have been trying to transform my data by logicle and inverse logicle transformations. However, even when I copy the logicle transformation parameters the software estimates, the transform function still does not work, and brings up the warning NAs introduced by coercion. I am wondering if I am defining my inputs in improper form? Could anyone help me out? An example is below: > > ------------------ > > samp <- read.FCSfile.name, transformation=FALSE) > lgcl <- estimateLogicle(samp, logchannels) > x <- transform(x,lgcl) > > Wset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$w > Tset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$t > Mset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$m > Aset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$a > > logicle <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset, 'logicle') > invLgcl <- inverseLogicleTransform(trans = logicle) > samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A")) > > ---------------------- > > The final line produces the warning: > > 1: In invLgcl("488-530/30-A") : NAs introduced by coercion > > Would anyone have an idea about what I might be doing incorrectly? I am new to R and flowCore, so it could be a basic problem I am overlooking. Thank you all so much for your help. > > Sincerely, > > Mark > PhD at ICL > > -----Original Message----- > From: Allenby, Mark > Sent: 10 July 2014 16:11 > To:bioconductor@r-project.org > Subject: FlowCore: Extracting parameters from estimateLogicle > > All, > > Is there a way to extract the A, T, M, W logicle parameters from the estimateLogicle function? > > i.e. lgcl <- estimateLogicle(samp, logchannels) and extract parameters estimated from lgcl. > > Mark > > > > ForwardedMessage.eml > > Subject: > [BioC] FlowCore: transform() NAs introduced by coercion > From: > "Allenby, Mark" <mark.allenby@imperial.ac.uk> > Date: > 07/10/2014 11:17 AM > > To: > "bioconductor@r-project.org" <bioconductor@r-project.org> > > > --------Sorry for double-posting, I didn't space my code properly------------ > > > > All, > > > > I have been trying to transform my data by logicle and inverse logicle transformations. However, even when I copy the logicle transformation parameters the software estimates, the transform function still does not work, and brings up the warning NAs introduced by coercion. I am wondering if I am defining my inputs in improper form? Could anyone help me out? An example is below: > > > > ------------------ > > > > samp <- read.FCSfile.name, transformation=FALSE) > > lgcl <- estimateLogicle(samp, logchannels) > > x <- transform(x,lgcl) > > > > Wset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$w > > Tset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$t > > Mset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$m > > Aset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$a > > > > logicle <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset, 'logicle') > > invLgcl <- inverseLogicleTransform(trans = logicle) > > samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A")) > > > > ---------------------- > > > > The final line produces the warning: > > > > 1: In invLgcl("488-530/30-A") : NAs introduced by coercion > > > > Would anyone have an idea about what I might be doing incorrectly? I am new to R and flowCore, so it could be a basic problem I am overlooking. Thank you all so much for your help. > > > > Sincerely, > > > > Mark > > PhD at ICL [[alternative HTML version deleted]]
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Mike and All, If you come back to this email, I have one more question for you. x <- transform(x, `405-525/50-A` = invLgcl(`405-525/50-A`)) I am trying to set a loop to transform all my parameter or channel names (such as `405-525/50-A`) which I have indexed by string. What I am currently trying and failing with is: for(i in 1:length(logchannels)){ x <- transform(x, as.name(logchannels[i]) = invLgclas.name(logchannels[i]))) } Error: unexpected '=' in: " invLgcl <- inverseLogicleTransform(trans = logicle) x <- transform(x, as.name(logchannels[i]) =" Any idea how to reference those parameter channels correctly? (logchannels is a vector of strings) Thanks for any help in advance, I'm going to post this to the group board as well. Mark From: Mike [mailto:wjiang2@fhcrc.org] Sent: 11 July 2014 18:43 To: bioconductor@r-project.org Cc: Allenby, Mark Subject: Re: FlowCore: transform() NAs introduced by coercion It can be fixed by using back tics instead of quote marks. i.e. samp <- transform(x, `488-530/30-A` = invLgcl(`488-530/30-A`)) On 07/11/2014 03:00 AM, bioconductor-request@r-project.org<mailto :bioconductor-request@r-project.org=""> wrote: Subject: [BioC] FlowCore: transform() NAs introduced by coercion From: "Allenby, Mark" <mark.allenby@imperial.ac.uk><mailto:mark.allenby@imperial.ac.uk> Date: 07/10/2014 11:14 AM To: "bioconductor@r-project.org"<mailto:bioconductor@r-project.org> <bioconductor@r-project.org><mailto:bioconductor@r-project.org> All, I have been trying to transform my data by logicle and inverse logicle transformations. However, even when I copy the logicle transformation parameters the software estimates, the transform function still does not work, and brings up the warning NAs introduced by coercion. I am wondering if I am defining my inputs in improper form? Could anyone help me out? An example is below: ------------------ samp <- read.FCSfile.name, transformation=FALSE) lgcl <- estimateLogicle(samp, logchannels) x <- transform(x,lgcl) Wset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$w Tset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$t Mset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$m Aset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$a logicle <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset, 'logicle') invLgcl <- inverseLogicleTransform(trans = logicle) samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A")) ---------------------- The final line produces the warning: 1: In invLgcl("488-530/30-A") : NAs introduced by coercion Would anyone have an idea about what I might be doing incorrectly? I am new to R and flowCore, so it could be a basic problem I am overlooking. Thank you all so much for your help. Sincerely, Mark PhD at ICL -----Original Message----- From: Allenby, Mark Sent: 10 July 2014 16:11 To: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: FlowCore: Extracting parameters from estimateLogicle All, Is there a way to extract the A, T, M, W logicle parameters from the estimateLogicle function? i.e. lgcl <- estimateLogicle(samp, logchannels) and extract parameters estimated from lgcl. Mark ForwardedMessage.eml Subject: [BioC] FlowCore: transform() NAs introduced by coercion From: "Allenby, Mark" <mark.allenby@imperial.ac.uk><mailto:mark.allenby@imperial.ac.uk> Date: 07/10/2014 11:17 AM To: "bioconductor@r-project.org"<mailto:bioconductor@r-project.org> <bioconductor@r-project.org><mailto:bioconductor@r-project.org> --------Sorry for double-posting, I didn't space my code properly------------ All, I have been trying to transform my data by logicle and inverse logicle transformations. However, even when I copy the logicle transformation parameters the software estimates, the transform function still does not work, and brings up the warning NAs introduced by coercion. I am wondering if I am defining my inputs in improper form? Could anyone help me out? An example is below: ------------------ samp <- read.FCSfile.name, transformation=FALSE) lgcl <- estimateLogicle(samp, logchannels) x <- transform(x,lgcl) Wset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$w Tset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$t Mset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$m Aset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$a logicle <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset, 'logicle') invLgcl <- inverseLogicleTransform(trans = logicle) samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A")) ---------------------- The final line produces the warning: 1: In invLgcl("488-530/30-A") : NAs introduced by coercion Would anyone have an idea about what I might be doing incorrectly? I am new to R and flowCore, so it could be a basic problem I am overlooking. Thank you all so much for your help. Sincerely, Mark PhD at ICL [[alternative HTML version deleted]]
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You should construct a 'transformList' for transforming multiple channels at a time. transList <- transformList(logchannels, invLgcl) x_trans <- transform(x, transList) On 07/11/2014 11:52 AM, Allenby, Mark wrote: > > Mike and All, > > If you come back to this email, I have one more question for you. > > x <- transform(x, `405-525/50-A` = invLgcl(`405-525/50-A`)) > > I am trying to set a loop to transform all my parameter or channel > names (such as `405-525/50-A`) which I have indexed by string. What I > am currently trying and failing with is: > > for(i in 1:length(logchannels)){ > > x <- transform(x, as.name(logchannels[i]) = > invLgclas.name(logchannels[i]))) > > } > > Error: unexpected '=' in: > > " invLgcl <- inverseLogicleTransform(trans = logicle) > > x <- transform(x, as.name(logchannels[i]) =" > > Any idea how to reference those parameter channels correctly? > (logchannels is a vector of strings) > > Thanks for any help in advance, I'm going to post this to the group > board as well. > > Mark > > [[alternative HTML version deleted]]
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