Hi Md.Mamunur

Thanks for reporting the problem. It does have problems of importing
detection and beadNum information due to the changes of Biobase package. ,
I have just fixed the problem in the release version lumi 1.10.2 and the
developing version, lumi 1.11.5.
It should be available to download after couple of days.


Pan



On 9/9/09 7:53 AM, "Md.Mamunur Rashid" <mamunur.rashid@kcl.ac.uk> wrote:

> Dear Dr. Pan Du,
> 
> Thanks for your reply.I am looking at the gene filter package. Hope I can find
> out a way around.
> The data I have, does contain detection column (column names : "Detection -
> 4765967022_A"......).
> I am using lumiR("file-name.txt",detectionTh = 0.01)function to read the file.
> But the 
> 
>> > pData(featureData(norm_object))$presentCount always return null
> 
> Is there anything special needed to be done to bring the detection information
> to the lumi Object??
> 
> I have also tried :
> data_raw <- 
> lumiR("Aneurist_Sample_Probe_Profile_Modified.txt",convertNuID=FALSE,inputAnno
> tation=FALSE, columnNameGrepPattern = list(exprs='AVG_SIGNAL',
> se.exprs='BEAD_STD', detection='Detection', beadNum='Avg_NBEADS'))
> 
> 
> I have a attached a snapshot of the data with the email ("showing the
> detection column"). please have a look.
> 
> *** This is a Illumina HumanHT12 chip data (produced by bead-studio) with 96
> samples. 
> While pre-processing the raw data I only have the following warning:
> 
> " There is no control probe information in the LumiBatch object
>   No background adjustment will be performed.
>   done.
> "
> Do you think this might have any significance in the above context.???
> 
> 
> Thanks in advance for your valuable help.
> 
> regards,
> Md.Mamunur Rashid
> 
> 
> On 09/08/2009 04:21 PM, Pan Du wrote:
>>   Re: Creating LumiBatch object from ExpressionSet Hi Mamun
>>  
>> For Illumina microarray, the detection p-value basically represents whether
>> the probe intensity is significant higher than the background level
>> (estimated based on the distribution of the negative control probes.). When
>> the p-value is lower than some threshold, for example, 0.05, we can claim
>> this probe is ³Present². If no measurement is ³Present² for the probe, we
>> usually consider it is not interest in our analysis and can be prefiltered.
>> Since your data has no detection p-value information, you have to use other
>> prefiltering method, such as those defined in genefilter package.
>>  
>> For your second question, I am not sure what exactly your question is. I read
>> your attached document. It looks fine for me.
>>  
>>  
>> Pan
>>  
>>  


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