Best package or code to filter Affymetrix probes by present calls??
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@garcia-orellanamiriam-5283
Last seen 7.1 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
Normalization gcrma Normalization gcrma • 708 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States
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 > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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