User: lhuang7

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lhuang710
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Location:
United States
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1 month, 4 weeks ago
Joined:
3 years, 4 months ago
Email:
l******@uchicago.edu
Lei Huang, Ph.D.
Senior Bioinformatician
Center for Research Informatics
University of Chicago

Posts by lhuang7

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Trouble loading 'lumi' package
... Hi Alexander, I am one of the lumi package maintainers. To the best of my knowledge, lumi was originally designed to process Illumina Methylation and Expression Microarrays and does not support HDF5Array at this point.  May I know the reason why you use both lumi and HDF5Array in your code? Could y ...
written 8 weeks ago by lhuang710
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Comment: C: Trouble loading 'lumi' package
... Hi Alexander, It seems no problem for me to load both lumi and HDF5Array package on my Mac OS. I guess the issue is more to do with HDF5Array than lumi on Windows system. Did you read this thread yet? https://support.bioconductor.org/p/108548/ Best, Lei   ...
written 8 weeks ago by lhuang710
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Job: Senior Bioinformatician at the University of Chicago
... We have an opening for a senior bioinformatician position at the Center for Research Informatics here in the University of Chicago. Please visit the following link if you are interested. Thanks! https://uchicago.wd5.myworkdayjobs.com/External/job/Hyde-Park-Campus/Senior-Bioinformatician_JR01794 ...
job bioinformatician job written 3 months ago by lhuang710
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Answer: A: Test for differential variability with missMethyl (DiffVar) using block design
... I got the similar warning message when calling varFit under a contrast design matrix setting (multiple comparison groups). > fitvar <- varFit(mval, design = design) Warning messages: 1: Partial NA coefficients for 466566 probe(s) The issue turns out to be a typo within the function varFit.defa ...
written 4 months ago by lhuang710
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Comment: C: New version of ChAMP can not proceed through champ.DMP
... I can confirm the error appears when the number of significant DMP is one. ...
written 13 months ago by lhuang710
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Comment: C: ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
... Thanks for the quick fix! ...
written 13 months ago by lhuang710
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Comment: C: ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
... Thanks Stephen! ...
written 13 months ago by lhuang710
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ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
... Hi, I try to create an annotation file using the function ParseMetaFromGtfFile() from SCAN.UPC package but get a warning message with no output file generated. After searching the archive I found this 3-year old post related to the same issue (https://support.bioconductor.org/p/59948/). The follo ...
annotation scan.upc written 13 months ago by lhuang710 • updated 13 months ago by Stephen Piccolo530
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Re: GenesAnswers for Arabidopsis!
... Dear Fuyou, As Dr. Gilbert Feng suggested, you can create a customized GeneAnswers object as explained in the package vignette (page 5) and R code chunk #3. Since you are interested in GO terms, the following solution might be what you want. Remember the second parameter in geneAnswersBuilder is an ...
annotation go geneanswers arabidopsis written 3.4 years ago by lhuang710

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