Respected Sir/ Madam, We the students of M.Sc.(BIOINFORMATICS), C.S.J.M. University, Kanpur (U.P), INDIA are encountering some errors regarding transcriptomic analysis of iron and phosphorus interaction in rice seedlings while using R-Package(2.12.2). We are using following commands for simpleaffy package:- >library(simpleaffy) > raw.data <- read.affy() Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './covdesc': No such file or directory We have already changed the directory but it is still showing the error. We shall be highly obliged to you. Thanking you. [[alternative HTML version deleted]]

Hi Umme, On Tue, Apr 19, 2011 at 1:43 PM, Umme Rummana <mbi_umme at="" yahoo.com=""> wrote: > Respected Sir/ Madam, > We the students of M.Sc.(BIOINFORMATICS), C.S.J.M. University, Kanpur (U.P), > INDIA are encountering some errors regarding transcriptomic analysis of iron and > phosphorus interaction in rice seedlings ?while using R-Package(2.12.2). We are > using following commands for simpleaffy package:- > >>library(simpleaffy) >> raw.data <- read.affy() > Error in file(file, "rt") : cannot open the connection > In addition: Warning message: > In file(file, "rt") : > ?cannot open file './covdesc': No such file or directory > > We have already changed the directory but it is still showing the error. > We shall be highly obliged to you. When you're in R and you type: R> dir() If you don't see your covdesc file along with your CEL files returned from that function call, than either will your call to "read.affy" -- and you also haven't "changed the directory." If I may (and I don't mean any offense): it seems that you are likely not very comfortable using R (no less bioconductor). You will find it very helpful if you spend some time to get more proficient working in the R environment. Take the time to go through "An Introduction to R" (google it), as well as "R Data Import/Export" (google that, too). After going through that, perhaps you'll be able to make more sense out of the vignettes that come with the bioconductor packages you are trying to use. As it stands now, it just seems like you're stabbing at the dark without taking the time to figure out what's *really* going on (you should be able to "translate" the error messages R is giving you, at the very least). This will quickly frustrate you as well as other people who are trying to help you. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact