Question: Microarray query
0
gravatar for Umme Rummana
7.9 years ago by
Umme Rummana40
Umme Rummana40 wrote:
Respected Sir/ Madam, We the students of M.Sc.(BIOINFORMATICS), C.S.J.M. University, Kanpur (U.P), INDIA are encountering some problems 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("covdesc.txt"); x.rma <- call.exprs(raw.data, "rma"); What are covdesc.txt file? How to create & where to save this covdesc.txt file for "transcriptomic analysis of iron and phosphorus interaction in rice seedlings" in Bioconductor(R-package)? We shall be highly obliged to you. Thanking you. [[alternative HTML version deleted]]
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ADD COMMENTlink modified 7.9 years ago by viritha kaza580 • written 7.9 years ago by Umme Rummana40
Answer: Microarray query
0
gravatar for viritha kaza
7.9 years ago by
viritha kaza580
viritha kaza580 wrote:
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/ins t/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]]
ADD COMMENTlink written 7.9 years ago by viritha kaza580
Answer: Microarray query
0
gravatar for viritha kaza
7.9 years ago by
viritha kaza580
viritha kaza580 wrote:
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/i nst/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]]
ADD COMMENTlink written 7.9 years ago by viritha kaza580
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/i nst/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]]
ADD REPLYlink written 7.9 years ago by Umme Rummana40
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]]
ADD REPLYlink written 7.9 years ago by viritha kaza580
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