[BioC] Beadarray readBeadSummaryData() problem

[Sean Davis]

On Thu, Jun 12, 2008 at 5:28 PM, ss <affysnp at 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 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
>>>
>>>
>>
>
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