[R] Errors in in my code

[jim holtman]

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 annotationtool 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
>
>
> --
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>
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>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?