User: Li Liu

gravatar for Li Liu
Li Liu100
Reputation:
100
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Trusted
Location:
Canada
Last seen:
4 years, 7 months ago
Joined:
5 years, 10 months ago
Email:
l******@hotmail.com

Posts by Li Liu

<prev • 13 results • page 1 of 2 • next >
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'DWD' method in 'inSilicoMerging' packages
... Hi, I want to use the 'DWD' method in the inSilicoMerging package to adjust batch effect of microarray gene expression data. I found the 'DWD' method is not included in the inSilicoMerging package now. Are there other package which can use perform the similar analysis easily?   Thanks,   Li ...
insilicomerging written 4.6 years ago by Li Liu100
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Comment: C: gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
... This is great! Thank you very much James. Li ...
written 4.6 years ago by Li Liu100
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gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
... Hi everyone, I have a microarray dataset which platform is 'Illumina HumanWG-6 v3.0 expression beadchip'. I want to know the corresponding gene symbols of each probeset. Where can I find the gene annotation files of this platform? I couldn't find it in there website. Thank you very much for your h ...
illumina written 4.6 years ago by Li Liu100 • updated 4.6 years ago by James W. MacDonald50k
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justRMA couldn't obtain CDF environment
... Dear members, I tried to read a batch of Affymetrix *.cel files and perform normalization using 'justRMA', but I got the following error: Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain OncoScan Library - package oncosc ...
cdf written 5.0 years ago by Li Liu100 • updated 5.0 years ago by James W. MacDonald50k
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FW: DWD method for batch effect removal
... From: liliu_1@hotmail.com To: dtenenba@fhcrc.org Subject: RE: [BioC] DWD method for batch effect removal Date: Thu, 8 Aug 2013 14:55:59 -0400 Hi Dan, Thank you very much. It works well now. Exciting! :) Now the only concern about this package is the new version still doesn't have those funct ...
written 5.9 years ago by Li Liu100 • updated 5.9 years ago by Dan Tenenbaum8.2k
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Comment: C: DWD method for batch effect removal
... Hi Dan, Thank you very much for the detail explanation. I agree it is better to wait for the new version. I saw the new version 1.4.1 was released now. However, it seems couldn't be downloaded. Thanks, Li > source("http://bioconductor.org/biocLite.R") > biocLite("inSilicoMerging") BioC_ ...
written 5.9 years ago by Li Liu100
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Comment: C: DWD method for batch effect removal
... Hi Dan, Thank you very much for the reply. I try to install the old version of DWD so I don't need to wait for tomorrow's new version. However I am not quite familiar the installation. After download should I put the compressed file "DWD_0.10.tar.gz" in a specific folder or I should unzipped it fi ...
written 5.9 years ago by Li Liu100
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DWD method for batch effect removal
... HI, I am using inSilicoMerging package to remove batch effect. A few merging methods, such as COMBAT, BMC, GENENORM, work well for me, so I suppose my dataset has no problem. However, when I use the method DWD, there is an error Error in is.factor(x) : object 'ybuf' not found Is there anybody who ...
insilicomerging written 5.9 years ago by Li Liu100 • updated 5.9 years ago by Dan Tenenbaum8.2k
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FW: fRMA package
... From: liliu_1@hotmail.com To: dtenenba@fhcrc.org Subject: RE: [BioC] fRMA package Date: Wed, 7 Aug 2013 12:23:16 -0400 Hi Dan, It works finally. Thank you very much for your nice help. Li > Date: Wed, 7 Aug 2013 06:43:23 -0700 > Subject: Re: [BioC] fRMA package > From: dtenenba@fhc ...
affxparser frma genomicranges written 5.9 years ago by Li Liu100
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Comment: C: fRMA package
... HI Dan, The following is what I run in R studio and the sessionInfo() output in window 7. Thanks. Li > source("http://bioconductor.org/biocLite.R") > biocLite("frma") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing pac ...
written 5.9 years ago by Li Liu100

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Popular Question 4.6 years ago, created a question with more than 1,000 views. For gene annotation of Illumina HumanWG-6 v3.0 expression beadchip

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