User: Li Liu
Li Liu • 100
- Reputation:
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- Location:
- Canada
- Last seen:
- 4 years, 7 months ago
- Joined:
- 5 years, 10 months ago
- Email:
- l******@hotmail.com
Posts by Li Liu
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... 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
...
written 4.6 years ago by
Li Liu • 100
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... This is great! Thank you very much James.
Li
...
written 4.6 years ago by
Li Liu • 100
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... 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 ...
written 4.6 years ago by
Li Liu • 100
• updated
4.6 years ago by
James W. MacDonald ♦ 50k
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... 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 ...
written 5.0 years ago by
Li Liu • 100
• updated
5.0 years ago by
James W. MacDonald ♦ 50k
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...
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 Liu • 100
• updated
5.9 years ago by
Dan Tenenbaum • 8.2k
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... 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 Liu • 100
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... 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 Liu • 100
0
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... 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 ...
written 5.9 years ago by
Li Liu • 100
• updated
5.9 years ago by
Dan Tenenbaum • 8.2k
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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 ...
written 5.9 years ago by
Li Liu • 100
0
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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 Liu • 100
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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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