[BioC] Best package or code to filter Affymetrix probes by present calls??

[Garcia Orellana,Miriam]

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 at 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