User: lhuang7

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lhuang730
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New User
Location:
United States
Last seen:
5 months, 1 week ago
Joined:
3 years, 10 months ago
Email:
l******@uchicago.edu
Lei Huang, Ph.D.
Senior Bioinformatician
Center for Research Informatics
University of Chicago

Posts by lhuang7

<prev • 12 results • page 1 of 2 • next >
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Answer: A: download data from GEO Illumina platform
... Hi Kan, You can use lumi package to do the analysis from the raw data (https://bit.ly/2C1lg2E). Best, Lei On Dec 9, 2018, at 2:36 PM, kankejia0703 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.o ...
written 4 months ago by lhuang730
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Answer: A: GSEA using TFs as the gene set
... If you are only interested in the DE genes from your data set, you could consider the over-representation test on your TF geneset. You can use the hypergeometric test implemented in enricher() function of the clusterProfiler package and MSigDB's C3 TFT geneset. HTH. ...
written 5 months ago by lhuang730
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Answer: A: lumi package fails to load because of a missing dependency (bumphunter)
... Hi kaur.alasoo, It looks like the bumphunter supported by Bioconductor 3.8 cannot be found at the current release page (https://www.bioconductor.org/packages/release/bioc/html/bumphunter.html). However, you can download the source code from the developer branch (https://www.bioconductor.org/package ...
written 5 months ago by lhuang730
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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 months ago by lhuang730
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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 months ago by lhuang730
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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 9 months ago by lhuang730
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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 11 months ago by lhuang730
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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 19 months ago by lhuang730
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Comment: C: ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
... Thanks for the quick fix! ...
written 19 months ago by lhuang730
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Comment: C: ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
... Thanks Stephen! ...
written 19 months ago by lhuang730

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