Re: [R] Errors in in my code

From: Christophe Lo <chriseverclear_at_hotmail.com>
Date: Sat, 08 Mar 2008 15:13:57 +0000

thank you so much. I must have spend a few hours last night trying to figure out.  

thank you again,
claire

> Date: Sat, 8 Mar 2008 09:13:31 -0500> From: jholtman_at_gmail.com> To: chriseverclear_at_hotmail.com> Subject: Re: [R] Errors in in my code> CC: r-help_at_r-project.org> > It says the file you are trying to access it not there. Do this in> two steps so you can see what is happening:> > fileName <- paste(dataDirectory, annotation_HGU133Plus2, sep = "/")> cat( fileName)> ... now use in it your read> > My guess is that what you think is in "annotation_HGU133Plus2" is not> the correct value.> > > On Sat, Mar 8, 2008 at 3:00 AM, Claire_6700 <chriseverclear_at_hotmail.com> wrote:> >> > Hi Everyone,> >> > I am very new to R. When i run the code yesterday, it was working fine. I> > was able to find gene annotation.> >> > somehow, today, when i try to run it again, it is giving me errors message> > that i don't understand. It says that it cannot open file. what file is it> > looking for?> >> > ######################################################> > ##make sure to install and load annotationt!

 ool in R> > annotation_HGU133Plus2 <- read.csv("c://affymetrix.csv", colClasses => > "character")> > annotation_probesets <- scan('c://ttest.csv',skip=1,what='')> > dataDirectory <- system.file("data", package = "annotationTools")> > annotation_stuff <- read.csv(paste(dataDirectory,> > annotation_HGU133Plus2, sep = "/"), colClasses = "character")> > myPS <- c(annotation_probesets)> > getGENESYMBOL(myPS, annotation_stuff)> > getGENEONTOLOGY(myPS, annotation_HGU133Plus2)> >> > ###############error message########################> > > annotation_stuff <- read.csv(paste(dataDirectory,> > + annotation_HGU133Plus2, sep = "/"), colClasses = "character")> > Error in file(file, "r") : unable to open connection> > In addition: Warning messages:> > 1: In file(file, "r") : only first element of 'description' argument used> > 2: In file(file, "r") :> > cannot open file> > 'C:/PROGRA~1/R/R-26~1.2/library/annotationTools/data/c("1007_s_at",> > "1053_at", "117_at", "121_at", "1255_g_at", "!
 1294_at", "1316_at", "1320_at",> > "1405_i_at", "1431_at", "1438_at", 
"1487_at", "1494_f_at", "1552256_a_at",> > "1552257_a_at", "1552258_at", "1552261_at", "1552263_at", "1552264_a_at",> > "1552266_at", "1552269_at", "1552271_at", "1552272_a_at", "1552274_at",> > "1552275_s_at", "1552276_a_at", "1552277_a_at", "1552278_a_at",> > "1552279_a_at", "1552280_at", "1552281_at", "1552283_s_at", "1552286_at",> > "1552287_s_at", "1552288_at", "1552289_a_at", "1552291_at", ', reason 'No> > such file or directory'> > >> >> > thank you,> > claire> >> >> > --> > View this message in context: http://www.nabble.com/Errors-in-in-my-code-tp15910042p15910042.html> > Sent from the R help mailing list archive at Nabble.com.> >> > ______________________________________________> > R-help@r-project.org mailing list> > https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code.> >> > > > -- > Jim Holtman> Cincinnati, OH>             !
 +1 513 646 9390       > > What is the problem you are trying to solve?
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