Hi there: I want to analyze a DNA microarray dataset that comes in ".txt" files. I actually have 3 different experiments and each one of them has 3 replicas. The format of these files is the following: Probe_ID Signal Detection Detection_pvalue Descriptions (the detection values are A,P, or M). My question is: Is there any function in Bioconductor to read this kind of file? (I have browsed several tutorials but haven't found anything to read files like these, most of the functions work with 'cel' files) Thank you for your help, Avhena [[alternative HTML version deleted]]

You can use "proper" R - try ?read.table --- On Thu, 11/2/10, avehna <avhena at="" gmail.com=""> wrote: > From: avehna <avhena at="" gmail.com=""> > Subject: [BioC] Reading xls affymetrix file? > To: bioconductor at stat.math.ethz.ch > Received: Thursday, 11 February, 2010, 11:31 AM > Hi there: > > I want to analyze a DNA microarray dataset that comes in > ".txt" files. I > actually have 3 different experiments and each one of them > has 3 replicas. > The format of these files is the following: > > Probe_ID? ???Signal? > ???Detection? > ???Detection_pvalue???Descriptions > > (the detection values are A,P, or M). > > My question is: Is there any function in Bioconductor to > read this kind of > file? > > (I have browsed several tutorials but haven't found > anything to read files > like these, most of the functions work with 'cel' files) > > Thank you for your help, > > Avhena > > ??? [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Avhena, As Moshe stated: the function in R called: read.table will work fine, but if you are actually asking how to work with your data using the BioConductor packages you will probably want to put your data into an ExpressionSet class object. To figure out how to do that the "expression set basics" tutorial should be quite helpful. best, noah On Feb 10, 2010, at 4:31 PM, avehna wrote: > Hi there: > > I want to analyze a DNA microarray dataset that comes in ".txt" files. I > actually have 3 different experiments and each one of them has 3 replicas. > The format of these files is the following: > > Probe_ID Signal Detection Detection_pvalue Descriptions > > (the detection values are A,P, or M). > > My question is: Is there any function in Bioconductor to read this kind of > file? > > (I have browsed several tutorials but haven't found anything to read files > like these, most of the functions work with 'cel' files) > > Thank you for your help, > > Avhena > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor