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 >> >> [[alternative HTML version deleted]]

Dear Dr. Pan Du, Thanks for the help. I will look forward for the upgraded package. regards, Mamun On 09/09/2009 02:42 PM, Pan Du wrote: > 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=F ALSE,inputAnnotation=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 “Present”. If no measurement is “Present” 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 > > [[alternative HTML version deleted]]