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

[James W. MacDonald]

Hi Miriam,

On 6/18/2012 3:40 PM, Garcia Orellana,Miriam wrote:
> 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

You already read the data in, using ReadAffy() above. There is no reason 
to do this again.

> 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

The error here is pretty clear; there isn't a file called 'covdesc' in 
your working directory.

As for filtering your data, have a look at the genefilter package.

Best,

Jim



>
>
>
>
> ********************************
> 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
>
>
>
>
>
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099