User: Weiwei Shi

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Weiwei Shi1.2k
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Posts by Weiwei Shi

<prev • 118 results • page 2 of 12 • next >
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hyperGTest
... Hi, I am wondering how to get all GO terms (actually for BP category) after I run hyperGTest? I need to know what GO terms were checked by hyperGTest. BTW, I used summary(x, pvalue=1.1) as a way to find the answer after I run hyperGTest for hgu133a, hgu133plus2 and hgu95av2. I found the numbers fo ...
go hgu133a hgu133plus2 hgu95av2 written 11.2 years ago by Weiwei Shi1.2k • updated 11.2 years ago by rgentleman5.5k
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Comment: C: a couple of questions on PGSEA package and GSEA
... Kyle, I agree with your reply to question 2 by calculating each "case" sample or interested sample's ratio versus a a median intensity from reference samples. However, my original question also mentioned what if the experimental design includes for example, different times, different concentration ...
written 11.3 years ago by Weiwei Shi1.2k
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a couple of questions on PGSEA package and GSEA
... Dear all, I have some questions relating to PGSEA package and GSEA method and hope to get some replies: 1. After reading the following paper, I think the theoretical basis for PGSEA is very different from GSEA (Broad, MIT). So, my first question is, is there a package in bioconductor running GSE ...
pgsea written 11.3 years ago by Weiwei Shi1.2k • updated 11.3 years ago by Furge, Kyle210
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Comment: C: similarity between two gene lists with varied length
... Actually, making this question more nontrivial is, 1. the lengths for the two gene lists are very different; 2. I could add another list as gene weight to any gene, for example, of union of two gene lists. On Sun, Aug 24, 2008 at 9:15 AM, Shannon, William wrote: > First thought is a similarity ...
written 11.3 years ago by Weiwei Shi1.2k
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similarity between two gene lists with varied length
... Dear listers, a little off-topic: I am looking for and compare algorithms which can calculate "distance" or "similarity" between two gene lists with different lengths. Any paper, any implementation in R and any suggestion is welcome! Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. ...
written 11.3 years ago by Weiwei Shi1.2k • updated 11.3 years ago by xie weibo50
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rgug4130a
... Hi, I have a question about an Agilent rat platform. We are studying a cross-platform issue and one of the platform is using G4130A, which bench scientists provide as limited information. I guess it is rgug4130a but how could I confirm this? what rgug stands for? btw, what's the difference between ...
annotation rgug4130a written 11.4 years ago by Weiwei Shi1.2k • updated 11.4 years ago by Marc Carlson7.2k
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a customized GO term
... Hi, I am wondering if I can make my own GO "term" and apply all utilities(packages, functions on GO terms) on my own versions? I mean, could I create GeneSet and GeneSet Collection as a collection of GO terms and perform some analysis like "hypergeometirc enrichment analysis" on my own "terms". T ...
go written 11.4 years ago by Weiwei Shi1.2k
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homology package question
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080313/ 5d779344/attachment.pl ...
written 11.8 years ago by Weiwei Shi1.2k • updated 11.8 years ago by James W. MacDonald52k
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Answer: A: Question to RankProd package
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written 12.0 years ago by Weiwei Shi1.2k
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biocLite to install a local binary sourced package for mac
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071207/ 2a5219e6/attachment.pl ...
written 12.0 years ago by Weiwei Shi1.2k • updated 12.0 years ago by lgautier@altern.org950

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Centurion 9.8 years ago, created 100 posts.

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