Thank you, Sean. It works. Yeah, the default skip is 8. The Illumina array data we received from the in-house microarray facility include raw data without background correction and pre-processed data after background correction. Can you recommend which one is better suited for beadarray package? I heard people suggested with less-processed data but apparently beadarray did not encompass a function to do background correction. Thank-you! Allen On Thu, Jun 12, 2008 at 5:30 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Thu, Jun 12, 2008 at 5:28 PM, ss <affysnp@gmail.com> wrote: > > i see. thank you, sean. that should be the problem. i have none of > > header information. the real data right starts from the second row > > with the first row for column names. i appreciate! allen > > Then, you will want skip=0. > > > On 6/12/08, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> On Thu, Jun 12, 2008 at 5:10 PM, ss <affysnp@gmail.com> wrote: > >>> Thank you, Sean. I will double check the help file. But, I do > >>> make the dataFile almost the same with the example file > >>> provided by beadarray package except that I have two columns > >>> in different order in my dataFile compared to the example file. > >>> I think 'skip parameter' is about to skip some header information > (rows) > >>> and it should not matter with columns. > >> > >> The skip parameter does matter. How many rows are there before your > >> column headings? The readBeadSummaryData assumes 8. Is that what you > >> have? > >> > >> Sean > >> > >>> On Thu, Jun 12, 2008 at 5:04 PM, Sean Davis <sdavis2@mail.nih.gov> > wrote: > >>>> > >>>> On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp@gmail.com> wrote: > >>>> > Hi all, > >>>> > > >>>> > I am using beadarray R package to analyze illumina array data and > have > >>>> > a > >>>> > problem > >>>> > with readBeadSummaryData(). > >>>> > > >>>> >> BSData = readBeadSummaryData(dataFile = dataFile) > >>>> > Error in readBeadSummaryData(dataFile = dataFile) : > >>>> > Could not find a column called ProbeID to use as bead identifiers. > >>>> > Check > >>>> > your file and try changing the 'ProbeID' and/or 'skip' arguments. > >>>> > > >>>> > The error said " Could not find a column called ProbeID to use... " > but > >>>> > I do > >>>> > have such column > >>>> > in the dataFile. Can anyone familiar with beadarray package suggest > how > >>>> > to > >>>> > get over this? > >>>> > >>>> Hi, Allen. It will probably help to read the help for the > >>>> readBeadSummaryData() function. You will need to look at the data > >>>> file that you have and decide what column will represent the unique > >>>> identifier for your arrays and assign that column name to the ProbeID > >>>> argument. Also, if you do not have a few rows of header information, > >>>> you may need to adjust the skip parameter. Since you say that you do > >>>> have a ProbeID column, the skip parameter may be the thing to change. > >>>> > >>>> Sean > >>> > >>> > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]