read.maimages & wt.fun

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gb606342000 ▴ 30

@gb606342000-3662

Last seen 9.6 years ago

Dear All, I am having problems to import genepix files. Does anyone have an idea what is going on? I use Mac OS X version 10.5.8. Please, see below. Thanks. Giovani This code DO NOT work: > f <- function(x) as.numeric(x$Flags > -1) > RG <- read.maimages(targets, source = "genepix", other.columns=list("Flags"), wt.fun = f) Error in gsub("\\.", "\\\\.", x) : input string 1 is invalid in this locale Removing the "wt.fun = f", works fine: > f <- function(x) as.numeric(x$Flags > -1) > RG <- read.maimages(targets, source = "genepix", other.columns=list("Flags")) Read 2009_04_02_4805_AXONe_PMT_Cy5_700_Cy3_0450_Lines_avg_0001.gpr Read 2009_05_08_4835g_AXON_PMT_Cy5_650_Cy3_0500_Lines_avg_0002_Multi.gpr > > sessionInfo() R version 2.9.2 (2009-08-24) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] limma_2.18.3 marray_1.22.0 loaded via a namespace (and not attached): [1] tools_2.9.2

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ADD COMMENT • link updated 14.6 years ago by Martin Morgan 25k • written 14.6 years ago by gb606342000 ▴ 30

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Martin Morgan 25k

@martin-morgan-1513

Last seen 3 days ago

United States

gb606342000 wrote: > Dear All, Hi Giovani -- > > I am having problems to import genepix files. Does anyone have > an idea what is going on? I use Mac OS X version 10.5.8. > > Please, see below. > > Thanks. Giovani > > > This code DO NOT work: >> f <- function(x) as.numeric(x$Flags > -1) >> RG <- read.maimages(targets, source = "genepix", other.columns=list("Flags"), wt.fun = f) > Error in gsub("\\.", "\\\\.", x) : > input string 1 is invalid in this locale You might arrange for your R to be the 'C' or 'en_US' locale, either with Sys.setlocale(locale="C") or (whether Sys.setlocale works seems to depend on OS), better, when you start R (in a bash shell this might be LC_ALL="C" R). I think the problem is that, in the en_US.UTF-8 locale, a '^2' is interpreted as a special symbol, not as two ascii characters. There's a long and probably more confusing than helpful post at https://stat.ethz.ch/pipermail/bioconductor/2007-July/018204.html Martin > Removing the "wt.fun = f", works fine: >> f <- function(x) as.numeric(x$Flags > -1) >> RG <- read.maimages(targets, source = "genepix", other.columns=list("Flags")) > Read 2009_04_02_4805_AXONe_PMT_Cy5_700_Cy3_0450_Lines_avg_0001.gpr > Read 2009_05_08_4835g_AXON_PMT_Cy5_650_Cy3_0500_Lines_avg_0002_Multi.gpr > >> sessionInfo() > R version 2.9.2 (2009-08-24) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > other attached packages: > [1] limma_2.18.3 marray_1.22.0 > > loaded via a namespace (and not attached): > [1] tools_2.9.2 > > _______________________________________________ > 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 COMMENT • link 14.6 years ago Martin Morgan 25k

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Hi Martin, I could solve the problem by running Sys.setlocale(locale="C") Just with that the code is working fine. Thank you very much for your help :-) Giovani --- On Sat, 9/5/09, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > Subject: Re: [BioC] read.maimages & wt.fun > To: "gb606342000" <gb606342000 at="" yahoo.com=""> > Cc: bioconductor at stat.math.ethz.ch > Date: Saturday, September 5, 2009, 11:04 AM > gb606342000 wrote: > > Dear All, > > Hi Giovani -- > > > > > I am having problems to import genepix files. Does > anyone have > > an idea what is going on? I use Mac OS X version > 10.5.8. > > > > Please, see below. > > > > Thanks. Giovani > > > > > > This code DO NOT work: > >> f <- function(x) as.numeric(x$Flags > -1) > >> RG <- read.maimages(targets, source = > "genepix", other.columns=list("Flags"), wt.fun = f) > > Error in gsub("\\.", "\\\\.", x) : > >???input string 1 is invalid in this > locale > > You might arrange for your R to be the 'C' or 'en_US' > locale, either with > > ? Sys.setlocale(locale="C") > > or (whether Sys.setlocale works seems to depend on OS), > better, when you > start R (in a bash shell this might be LC_ALL="C" R). I > think the > problem is that, in the en_US.UTF-8 locale, a '^2' is > interpreted as a > special symbol, not as two ascii characters. > > There's a long and probably more confusing than helpful > post at > > https://stat.ethz.ch/pipermail/bioconductor/2007-July/018204.html > > Martin > > > > Removing the "wt.fun = f", works fine: > >> f <- function(x) as.numeric(x$Flags > -1) > >> RG <- read.maimages(targets, source = > "genepix",? other.columns=list("Flags")) > > Read > 2009_04_02_4805_AXONe_PMT_Cy5_700_Cy3_0450_Lines_avg_0001.gpr > > > Read > 2009_05_08_4835g_AXON_PMT_Cy5_650_Cy3_0500_Lines_avg_0002_Multi.gpr > > > > >> sessionInfo() > > R version 2.9.2 (2009-08-24) > > i386-apple-darwin8.11.1 > > > > locale: > > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] stats? ???graphics? > grDevices utils? ???datasets? > methods? > > [7] base? ??? > > > > other attached packages: > > [1] limma_2.18.3? marray_1.22.0 > > > > loaded via a namespace (and not attached): > > [1] tools_2.9.2 > > > > _______________________________________________ > > 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 > >

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