Hi Umme, Try once by using >raw.data <- read.affy("covdesc.txt") # or what ever you have named the description file as. not just read.affy(). I just tested this on some cell files with the description file and it works. You can read this document. This might be helpful http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/ProtocolSimpleaffy. txt code that I used were mostly from the above file: >source("http://bioconductor.org/biocLite.R") > biocLite("simpleaffy") > library(simpleaffy) # this loaded the affy and biobase packages as well # changed directory to my working directory where I have the description file and the cel files. > raw.data <- read.affy("covdesc.txt") >x.rma <- call.exprs(raw.data, "rma") > write.exprs(x.rma, file="rma_affy_all.txt") Regards, Viritha On Thu, Apr 21, 2011 at 8:46 PM, Umme Rummana <mbi_umme@yahoo.com> wrote: > Hi Viritha, > We tried the commands that u told us, but our working directory is > C:/Users/bi302/Documents only. Can you please tell us the exact stepwise > procedure of the microarray analysis using R-Package. So that we can check > out what we have performed till yet. Please tell us what are the things > necessary before starting microarray analysis using R-Package(2.12.2). > > ------------------------------ > *From:* viritha kaza <viritha.k@gmail.com> > *To:* Umme Rummana <mbi_umme@yahoo.com> > *Cc:* bioconductor@r-project.org > *Sent:* Thu, April 21, 2011 12:22:20 AM > *Subject:* Re: Microarray query > > Hi Umme, > I still think that this error may be due to the fact that your working > directory may not been set to "C:/Users/bi302/Documents" > just check if your working directory is where your files are, using > >getwd() > if it doesnot show as your default directory (C:/Users/bi302/Document) then > use > >setwd("C:/Users/bi302/Documents") > and then use read.affy() > I see this exact error message when my working directory is not set to > where my files are. > Hope this helps! > Regards, > Viritha > > > On Wed, Apr 20, 2011 at 3:21 AM, Umme Rummana <mbi_umme@yahoo.com> wrote: > >> Hello Viritha, >> We tranfered our celfiles and covdesc files to the default >> directory C:/Users/bi302/Documents. Still it's showing the same error. We >> still not get how to proceed further in our Microarray analysis project >> using R-package(2.12.2). >> >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 >> >> >> ------------------------------ >> *From:* viritha kaza <viritha.k@gmail.com> >> *To:* Umme Rummana <mbi_umme@yahoo.com> >> *Cc:* bioconductor@r-project.org >> *Sent:* Mon, April 18, 2011 7:28:39 PM >> *Subject:* Re: Microarray query >> >> Hi Umme, >> With a little experience that I have I can tell you that you can get more >> information here at >> >> http://www.bioconductor.org/packages/2.6/bioc/vignettes/simpleaffy/ inst/doc/simpleAffy.pdf >> From the above file it tells that covdesc is default file. In page 3 you >> can see how the file looks, this file describes your cell files. You can >> understand more by reading above file. >> Coming to where to store this file, You can store the data in any >> directory but only specify where the file is stored. >> If using the Rgui >> (use \File -> Change Dir"menu item). >> >> otherwise commands like setwd() can help you are set the working >> directory. >> >> Hope this helps, >> >> Regards, >> >> Viritha >> >> > > [[alternative HTML version deleted]]