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Flow Cytometry Analysis with FlowCore

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I wanna know how to do transformation of the channel four (FLH 4) without using the standard transformations offer by the flowCore package? The values of the channel four are between 1 and 4096 and i need to convert in values between 1 and 246 with the rule 10^(x/1024). Thank you. -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 LC_MONETARY=Portuguese_Portugal.1252 [4] LC_NUMERIC=C LC_TIME=Portuguese_Portugal.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 flowViz_1.22.0 lattice_0.20-15 flowCore_1.24.2 [6] rrcov_1.3-3 pcaPP_1.9-49 mvtnorm_0.9-9995 robustbase_0.9-8 Biobase_2.18.0 [11] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] feature_1.2.8 graph_1.36.2 grid_2.15.1 hexbin_1.26.2 IDPmisc_1.1.17 KernSmooth_2.23-10 [7] ks_1.8.12 MASS_7.3-23 stats4_2.15.1 tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 11.5 years ago by Jiang, Mike ▴ 20 • written 11.5 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2013-07-03

This will do: |> samp <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore")) > apply(exprs(samp),2,range) FSC-H SSC-H FL1-H FL2-H FL3-H FL1-A FL4-H Time [1,]85 11 1.000 1 1.000 0 1.000 1 [2,]1023 1023 3681.141 10000 3304.164 1023 9910.371 626 > samp.trans <- transform(samp, trans.FL4.H =10^(`FL4-H`/1024)) > apply(exprs(samp.trans),2,range) FSC-H SSC-H FL1-H FL2-H FL3-H FL1-A FL4-H Time trans.FL4.H [1,]85 11 1.000 1 1.000 0 1.000 1 1.002251e+00 [2,]1023 1023 3681.141 10000 3304.164 1023 9910.371 626 4.765375e+09| Mike Jiang On 07/03/2013 04:10 AM, Telma Fernandes [guest] wrote: > I wanna know how to do transformation of the channel four (FLH 4) without using the standard transformations offer by the flowCore package? > > The values of the channel four are between 1 and 4096 and i need to convert in values between 1 and 246 with the rule 10^(x/1024). > > Thank you. > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 LC_MONETARY=Portuguese_Portugal.1252 > [4] LC_NUMERIC=C LC_TIME=Portuguese_Portugal.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 flowViz_1.22.0 lattice_0.20-15 flowCore_1.24.2 > [6] rrcov_1.3-3 pcaPP_1.9-49 mvtnorm_0.9-9995 robustbase_0.9-8 Biobase_2.18.0 > [11] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] feature_1.2.8 graph_1.36.2 grid_2.15.1 hexbin_1.26.2 IDPmisc_1.1.17 KernSmooth_2.23-10 > [7] ks_1.8.12 MASS_7.3-23 stats4_2.15.1 tools_2.15.1 > > -- > Sent via the guest posting facility at bioconductor.org. [[alternative HTML version deleted]]

score 0 · Answer 2 · 2013-07-04

`exprs` method is for `flowFrame`, not `flowSet`. type`help(exprs)` for more details. ________________________________ From: Telma Fernandes [telma.7919@gmail.com] Sent: Thursday, July 04, 2013 12:47 AM To: Jiang, Mike Subject: Re: Flow Cytometry Analysis with FlowCore Thank you so much but I have a problem with the function exprs. I allways have this message: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "exprs", for signature "flowSet" Telma Fernandes 2013/7/3 Mike <wjiang2@fhcrc.org<mailto:wjiang2@fhcrc.org>> This will do: > samp <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore")) > apply(exprs(samp),2,range) FSC-H SSC-H FL1-H FL2-H FL3-H FL1-A FL4-H Time [1,] 85 11 1.000 1 1.000 0 1.000 1 [2,] 1023 1023 3681.141 10000 3304.164 1023 9910.371 626 > samp.trans <- transform(samp, trans.FL4.H = 10^(`FL4-H`/1024)) > apply(exprs(samp.trans),2,range) FSC-H SSC-H FL1-H FL2-H FL3-H FL1-A FL4-H Time trans.FL4.H [1,] 85 11 1.000 1 1.000 0 1.000 1 1.002251e+00 [2,] 1023 1023 3681.141 10000 3304.164 1023 9910.371 626 4.765375e+09 Mike Jiang On 07/03/2013 04:10 AM, Telma Fernandes [guest] wrote: I wanna know how to do transformation of the channel four (FLH 4) without using the standard transformations offer by the flowCore package? The values of the channel four are between 1 and 4096 and i need to convert in values between 1 and 246 with the rule 10^(x/1024). Thank you. -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 LC_MONETARY=Portuguese_Portugal.1252 [4] LC_NUMERIC=C LC_TIME=Portuguese_Portugal.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 flowViz_1.22.0 lattice_0.20-15 flowCore_1.24.2 [6] rrcov_1.3-3 pcaPP_1.9-49 mvtnorm_0.9-9995 robustbase_0.9-8 Biobase_2.18.0 [11] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] feature_1.2.8 graph_1.36.2 grid_2.15.1 hexbin_1.26.2 IDPmisc_1.1.17 KernSmooth_2.23-10 [7] ks_1.8.12 MASS_7.3-23 stats4_2.15.1 tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. [[alternative HTML version deleted]]