[BioC] Beadarray readBeadSummaryData() problem

[ss]

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

On 6/12/08, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Thu, Jun 12, 2008 at 5:10 PM, ss <affysnp at 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 at mail.nih.gov> wrote:
>>>
>>> On Thu, Jun 12, 2008 at 4:23 PM, ss <affysnp at 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
>>
>>
>