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Garcia Orellana,Miriam
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@garcia-orellanamiriam-5283
Last seen 10.3 years ago
Ben:
I followed the steps you gave and the working directory was well set
but I still getting the same problem, next is the detail of what I
got. Please anyone having other idea of this wrong warning or other
approach to filter my data. Thanks.
> library(simpleaffy)
> library(gcrma)
> getwd()
[1] "C:/Users/miriam/Documents/1studytemp/RESULTS/liver2008
gene/CEL_files"
> dir()
[1] "4367.CEL" "4368.CEL" "4381.CEL"
"4384.CEL"
[5] "4387.CEL" "4388.CEL" "4394.CEL"
"4395.CEL"
[9] "4396.CEL" "4398.CEL" "4399.CEL"
"4400.CEL"
[13] "4402.CEL" "4404.CEL" "4409.CEL"
"4410.CEL"
[17] "4413.CEL" "4429.CEL"
"affymetrix_gcrma.txt" "covdesc.prn"
[21] "DD_CD.txt" "eset.gcrma.Rdata"
> raw.data <- ReadAffy()
> gcrma.eset <- call.exprs(raw.data, "gcrma")
Adjusting for optical effect..................Done.
Computing affinities.Done.
Adjusting for non-specific binding..................Done.
Normalizing
Calculating Expression
> raw.data <- read.affy() ##read data in working directory
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
> raw.data<- read.affy("covdesc")
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
********************************
Miriam Garcia, MS
PhD candidate
Department of Animal Sciences
University of Florida
________________________________________
From: Ben Tupper [btupper@bigelow.org]
Sent: Monday, June 18, 2012 2:30 PM
To: Garcia Orellana,Miriam
Subject: Re: [BioC] Best package or code to filter Affymetrix probes
by present calls??
Hi,
On Jun 18, 2012, at 12:46 PM, Garcia Orellana,Miriam wrote:
Dear R users:
First thank to all users for their direct or indirect support with
previous question. Now. I am rephrasing this question since I did not
get any help the last 3 days. I am having hard time to analyze my
microarray data, since the use of R environment is a new world for me.
I have 18 affymetrix bovine arrays from liver samples of 30d old
calves that born from cows fed 3 types of prepartum dam diets (factor
DD, 6 arrays per DD) and were fed just milk replacer the first 30d of
life ( factor MR, 9 array per MR). Biologically I will expect that the
main factor driving any difference will be the MR rather than the DD
(unless some imprinting genes are expressed).
So I have the idea to filter non expressed genes using the simpleaffy
package using the manual but I don't know what is wrong when I try to
load the covdesc file I got error.
I have a folder in my directory that contains all 18 CEL files and
also the covdesc (extension .prn - is this the right one?). Since I
was able to run the gcrma normalization so the working directory maybe
well set, what I got is the next when using the option read.affy to
read the covdesc file.
> raw.data <- ReadAffy()
> gcrma.eset <- call.exprs(raw.data, "gcrma")
Loading required package: AnnotationDbi
Adjusting for optical effect..................Done.
Computing affinities.Done.
Adjusting for non-specific binding..................Done.
Normalizing
Calculating Expression
> raw.data <- read.affy() ##read data in working directory
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
> raw.data<- read.affy("covdesc")
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
I would really appreciate if you can suggest me any simple method to
filter my genes ( I want to keep probes that are present in at least
4 of the 9 arrays in at least one of the MR groups, or do you think I
should consider the interaction prepartum diet * milk replacer (then 3
arrays per interaction group and try to have at least 2 present genes
in at least 1 of the 6 interactions)
Thanks in advance for any help.
Miriam
Try to confirm that the current working directory is where you think
it is...
> getwd()
If not then you'll need to use setwd() to set the correct directory.
If your R session 'resides' in your desired directory, then check that
the contents of the directory include what read.affy() expects...
> dir()
Cheers,
Ben
Ben Tupper
Bigelow Laboratory for Ocean Sciences
180 McKown Point Rd. P.O. Box 475
West Boothbay Harbor, Maine 04575-0475
http://www.bigelow.org
