User: Pan Du

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Pan Du440
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Posts by Pan Du

<prev • 44 results • page 2 of 5 • next >
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Answer: A: import only partial samples of an array
... Hi Chris There is another function: lumiR.batch for you purpose. You can define the samples you want to input in the "sampleInfoFile" parameter. Check the help of "lumiR.batch" for more details. Pan On Wed, Aug 28, 2013 at 6:47 AM, Chris [guest] wrote: > > Hi, I was wondering whether it ...
written 6.1 years ago by Pan Du440
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Answer: A: lumiR returns ExpressionSet object instead of LumiBatch
... Hi Liu X This is because your data does not include the bead standard error information for the probes (columns are named like "BEAD_STDERR"), which is required for LumiBatch class. If this information is missing, the lumiR will just output an ExpressionSet object. Please check the help of lumiR an ...
written 6.3 years ago by Pan Du440
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Answer: A: detectionCall usefulness
... Hi Francisco I believe this is because limma needs to estimate the background variation. The filtered unexpressed genes have lower variation. After you filtered them, the estimated background variation will be higher, which may result in a shorter list of differentially expressed genes. You can che ...
written 6.4 years ago by Pan Du440
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Answer: A: How do I background correct an Illumina eset without using lumiB?
... Hi Emma By default, lumiB estimates the background level based on the negative control probes if they were included in the controlData slot. Because the beads of each probe are randomly distributed over the chip surface, the spatial effects are ignored during the background adjustment. By default, ...
written 6.4 years ago by Pan Du440
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Answer: A: Lumi problem - 'Annotation columns not available'
... Hi Atul I have found the reason. Your data file includes control data together with the expression data. Because the control data includes no annotation information (that's not a problem), lumiR outputted the message. So no problem for your data file and lumiR output. I will update the code of in ...
written 6.5 years ago by Pan Du440
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Comment: C: Lumi problem - 'Annotation columns not available'
... Hi Atul I just had a quick try of the example data you sent. It works pretty well. Here is my command: test <- lumiR('FinalReport_sample.txt', annotationColumn = c('PROBE_ID','ACCESSION','SYMBOL','ENTREZ_GENE_ID','PROBE_START','CHRO MOSOME')) If you still have problems, change the error option ...
written 6.5 years ago by Pan Du440
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Answer: A: Lumi problem - 'Annotation columns not available'
... Hi Atul Can you send me to the top 100 rows of your data file? I cannot tell the reason without seeing your data. Thanks for reporting this! Pan Date: Mon, 22 Apr 2013 13:28:21 -0400 From: Atul Kakrana To: "bioconductor@r-project.org" Subject: [BioC] Lumi problem - 'Annotation columns not avai ...
written 6.5 years ago by Pan Du440
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Bug in biocLite?
... Hi Dan I just tried to install packages using "biocLite" for my Mac computer. When I ran biocLite(), it returns the following error: 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.12/bioc, using ' http://bioconductor.org/packages/2.12/bioc' Error: 'BiocInstaller' pack ...
written 6.5 years ago by Pan Du440 • updated 6.5 years ago by Dan Tenenbaum8.2k
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Answer: A: genoset:::initGenoSet
... Hi Leonard Pete has fixed this problem in the developing version of genoset. Thanks for reporting this! Pan On Wed, Feb 20, 2013 at 4:27 AM, Schalkwyk, Leonard wrote: > > > When generating a MethyGenoSet to try out the methyAnalysis package, I got the following: > > > c ...
written 6.6 years ago by Pan Du440
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Answer: A: Loading Data into MethyAnalysis
... Hi Ranya The vignette of MethyAnalysis package needs to be further improved. I will update it within next couple of weeks when I have time. As for creating MethyGenoSet objects, you can either use MethyGenoSet() function or converted them from MethyLumiM objects using MethyLumiM2GenoSet function, w ...
written 6.7 years ago by Pan Du440

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