Hi Sean,

actually I remember that my script more or less worked on the same file in
an old R version.

in fact, with the configuration provided at the end of the mail, everything
works properly. so I think it is not a problem in the imput data, but in the
handling of the data


> sessionInfo()
R version 2.5.1 (2007-06-27)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
    lumi annotate     mgcv     affy   affyio  Biobase
 "1.2.0" "1.14.1"  "1.4-1" "1.14.2"  "1.4.1" "1.14.1"


On Tue, Nov 4, 2008 at 5:54 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> On Tue, Nov 4, 2008 at 8:45 AM, John Lande <john.lande77@gmail.com> wrote:
>
>> On Tue, Nov 4, 2008 at 12:04 PM, John Lande <john.lande77@gmail.com>
>> wrote:
>>
>> > dear all,
>> >
>> > I am using lumi to normalize raw Illumina Data, but when I run the
>> script,
>> > I retrive this error. can you help me?
>> >
>> > library(lumi)
>> >
>> > r=lumiR("gene_expression.txt")
>> >
>> > b=lumiB(r, method="bgAdjust")
>> >
>> > Perform bgAdjust background correction ...
>> > There is no control probe information in the LumiBatch object!
>> > No background adjustment will be performed.
>> >
>> > thank you
>> >
>>
>> maybe it is just a problem of annotation, thereby I added the library
>> annotation when I import data:
>>
>
> No.  It is that you did not include control probe information in the
> exported data from beadstudio, so lumi has no idea what the background is.
>
>
>>
>> > r=lumiR("Breast_86.txt", lib = "lumiHumanIDMapping.db")
>> Annotation columns are not available in the data.
>> Perform Quality Control assessment of the LumiBatch object ...
>> Error in names(mapping.new) <- inputID.bak :
>>  'names' attribute [24354] must be the same length as the vector [24350]
>>
>> but again another error...
>>
>
> You'll need to determine the annotation package that goes with your chip.
> For illumina, there are a number of choices, so you'll have to choose the
> right one based on the chip and the ID that you want to map.  The
> lumiHumanIDMapping.db package simply maps between different human chips and
> does not provide annotation.  What you have tried here cannot work.
>
> Sean
>
>
>

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