[BioC] Beadarray readBeadSummaryData() problem

[Sean Davis]

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
>
>