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]]
