-------- Original Message -------- Subject: Re: Creating LumiBatch object from ExpressionSet Date: Wed, 9 Sep 2009 13:53:42 +0100 From: Md.Mamunur Rashid <mamunur.rashid@kcl.ac.uk> To: Pan Du <dupan at="" northwestern.edu="">, "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> 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",convertN uID=FALSE,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: > 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 > > > On 9/7/09 9:34 AM, "Md.Mamunur Rashid" <mamunur.rashid at="" kcl.ac.uk=""> wrote: > > Dear Dr. Pan Du, > Thanks for your response. Please accept my apology for replying so > late. The object AP seems a numeric list of all the genes > detection values > (mean from all samples).Can you please give a bit further > elaboration about > how "AP" can be used to extract the genes expressed under p.value > threshold ??? > > More over a have few more questions. I would be really helpful if > you can give > me some suggestions regarding the problems. > > > I am working with a set of illumina microarray data (96 samples) > from three groups > (i.e. group-1(X),group-2(Y),group-3(Z)). 32 samples from each group. > > I have read the data using lumiR method and processed the data > using lumi Methods.(lumiE) > Now I need to identify the differentially expressed genes by > comparing each of these groups > with each other. I am using linear model in limma package and > topTable method to identify > top N differentially expressed genes.(please have a look at the > attachments). > > ***I have attached a file containing (1. The code, 2. result of > the top-table, 3. Array weights > > Thanks in advance. > > regards, > mamun > > > > > > Sincerely, > Md.Mamunur Rashid > > > > On 07/31/2009 05:16 PM, Pan Du wrote: > > > Hi Md.Mamunur, > > Functions lumiQ and detectionCall does not support > ExpressionSet objects > because they need some information not included in > ExpressionSet class by > default. For example, both detectionCall and lumiQ function > need to use the > data matrix included in the "detection". > > If you ExpressionSet object do include "detection", here is > the alternative > way to estimate number of detection calls of each probe: > > detect <- get('detection', assayData(lumi.T)) > ## suppose you claim p-value less than 0.05 as a detection call > AP <- rowSums(detect <= 0.05) > > Hope this is helpful to you, > > > Pan > >