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>

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 

 


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>

>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 

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