User: Pan Du

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Pan Du1.2k
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Posts by Pan Du

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Answer: A: Lumi: LumiT vst transform error
... Hi Sarah After checking your data, I found the data has already log2 transformed. The VST transformation should be on the raw scale. So please convert your data to raw scale first, then you can apply vst. exprs(x.lumi) <- 2^(exprs(x.lumi)) I will also add checking code in the lumi package to g ...
written 6.7 years ago by Pan Du1.2k
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Answer: A: Lumi: LumiT vst transform error
... Hi Sarah The information you provided is too limited, I cannot answer your question. At least, you need to provide sessionInfo() and the information of lumi.B. You can also send me a subset of lumi.B, for example, test = lumi.B[1:5000,] save(test, file='test.Rdata') and send me 'test.Rdata' fil ...
written 6.7 years ago by Pan Du1.2k
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Question regarding background correction in lumi package
... Hi Jeanie > Hi Dr. Pan, > > I am trying to use lumi package on the microarray data. My questions are: > > Q1. If I understand it right, the Beadstudio output data has to be > background corrected then read in with lumiR, right? Then what does > 'bgAdjust' do in lumiB on an alr ...
microarray lumi written 6.8 years ago by Pan Du1.2k
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Comment: C: Adding Illumina GEO GPL IDs to IlluminaIDMapping?
... Thanks! Sean I found the gpl table in the GEOmetadb.sqlite database has already included all information of GEO platforms. So adding a function of matching GPL ID in GEOmetadb will be helpful for users not familiar with SQL. The input parameter can include manufacturer, organism, data_row_count and ...
written 6.8 years ago by Pan Du1.2k
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Adding Illumina GEO GPL IDs to IlluminaIDMapping?
... Hi Denise Thanks for your suggestion. I agree it will be help to include GEO GPL IDs for different Illumina chips in the IlluminaIDMapping annotation package. If you have the mapping available, could you send me the list? So I don't need to search again. I will add an additional table for this in t ...
systemsbiology lumi written 6.8 years ago by Pan Du1.2k • updated 6.8 years ago by Sean Davis21k
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lumiR produces Expression set, not lumi batch
... Hi Tom I believe it is because your data doesn¹t include the ³BEAD_STD² columns, which is required for the LumiBatch class. So please ask your data provider include the ³BEAD_STD² columns. If not, please just go ahead and use log2 transformation instead of ³vst² transformation. All other procedures ...
go written 6.8 years ago by Pan Du1.2k
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Comment: C: lumi for Illumina methylation data - understanding the colour adjustment
... Hi Lavinia You are right. For Infinium methylation chip, the methylated and unmethylalted probes are always in the same color channel. When performing non-linear color adjustment (like quantile or other curve fitting methods), the ratio of methylated and unmethylalted probe intensities may change. ...
written 6.9 years ago by Pan Du1.2k
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lumi for Illumina methylation data - understanding the colour adjustment
... Hi Lavinia It is hard to answer your question without knowing the quality of your data. My suggestion is performing visually color bias check first before applying color bias adjustment. If the color bias is not severe, then only perform conservative adjustment (scaling and shift adjust) or not per ...
microarray normalization probe written 6.9 years ago by Pan Du1.2k • updated 6.9 years ago by Lavinia Gordon480
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Merging bioconductor lumi annotations with lumi output
... Hi Thomas You can change the default inputted annotation columns by setting the "annotationColumn" parameter of lumiR function. These annotation information will be kept in the "featureData" of ExpressionSet (or LumiBatch) object. One thing I am not sure is what kind of IDs is used for your Genome ...
annotation probe lumi written 6.9 years ago by Pan Du1.2k
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Modeling of methylation status using lumi
... Hi Gilles Thanks for your feedback of the newly implemented Methylation functions in the lumi package. As for the functions of modeling methylation status, I will organize and upload them to the developing version within next few weeks, hopefully by the end of this year. For the Illumina 450k methy ...
microarray lumi brain written 6.9 years ago by Pan Du1.2k

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