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Question: problem with beadarray package 2.0
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gravatar for Daniela Albrecht
6.6 years ago by
Daniela Albrecht10 wrote:
Dear bioconductor people. I am using the beadarray package for working with Illumina bead data. In beadarray version 1.4 following code works fine for reading the data: /targets=read.table(file="./5645810041_txt- Datein/targets.txt",header=T) a<-readIllumina(path="./5645810041_txt- Datein",arrayNames=targets[,"ArrayName"],useImages=F,metrics=T, textType=".csv",metricsFile="./5645810041/Metrics.txt")/ With the new beadarray version 2.02. It does not work anymore. With a simplified code line /a<-readIllumina(useImages=F,metrics=T)/ it says cannot open path/5645810041_txt-Datein/NA no such file or directory. How do I have to specify the filename, so it does not want to open a file named "NA.txt"? By the way, if I rename my first datafile in NA.txt, it says Unknown input format! Expected 4 columns for single channel data or 7 columns for two channel data This is how my file looks like (I also tried to change the , into tab but it does not work either: Illumicode,N,Mean GRN,Dev GRN 10008,36,646,124 10010,17,91,21 10014,12,72,11 10017,19,83,17 10019,30,216,39 ... Thanks in advance for your help Daniela [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.6 years ago by Tim Triche4.2k • written 6.6 years ago by Daniela Albrecht10
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gravatar for Tim Triche
6.6 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
You are trying to read in CSV files. Beadarray isn't really meant to handle these (as far as I know) because they have already been summarized by Illumina's software. The text files that 'beadarray' expects have one line per bead, usually with X and Y coordinates as well. I can send you code to handle this type of input, but really you are better off using the raw data (if these are expression arrays) or the .idat files (if these are SNP or methylation arrays) and my intention is to make the latter more amenable to both by using oligoClasses in the near future. Illumina's file format nightmare is not doing anyone any favors, IMHO. --tim On Mon, Dec 6, 2010 at 3:18 AM, Daniela Albrecht < daniela.albrecht@biocontrol-jena.com> wrote: > Dear bioconductor people. > > I am using the beadarray package for working with Illumina bead data. In > beadarray version 1.4 following code works fine for reading the data: > > /targets=read.table(file="./5645810041_txt- Datein/targets.txt",header=T) > > a<-readIllumina(path="./5645810041_txt- Datein",arrayNames=targets[,"ArrayName"],useImages=F,metrics=T, > textType=".csv",metricsFile="./5645810041/Metrics.txt")/ > > With the new beadarray version 2.02. It does not work anymore. With a > simplified code line > > /a<-readIllumina(useImages=F,metrics=T)/ > > it says cannot open path/5645810041_txt-Datein/NA no such file or > directory. > > How do I have to specify the filename, so it does not want to open a > file named "NA.txt"? By the way, if I rename my first datafile in > NA.txt, it says > > Unknown input format! > Expected 4 columns for single channel data or 7 columns for two channel > data > > This is how my file looks like (I also tried to change the , into tab > but it does not work either: > > Illumicode,N,Mean GRN,Dev GRN > 10008,36,646,124 > 10010,17,91,21 > 10014,12,72,11 > 10017,19,83,17 > 10019,30,216,39 > ... > > Thanks in advance for your help Daniela > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD COMMENTlink written 6.6 years ago by Tim Triche4.2k
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