[BioC] FlowCore: transform() NAs introduced by coercion

[Allenby, Mark]

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:

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samp <- read.FCS(file.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"))

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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