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
> >>>
> >>>
> >>
> >
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> >
>

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