User: Roger Liu

gravatar for Roger Liu
Roger Liu260
Reputation:
260
Status:
Trusted
Location:
Last seen:
9 years, 5 months ago
Joined:
12 years, 4 months ago
Email:
z******@gmail.com

Posts by Roger Liu

<prev • 26 results • page 1 of 3 • next >
0
votes
3
answers
753
views
3
answers
Answer: A: where is the "getHomolog" function in biomaRt?
... I figured it out, it depends on what version you used. My linux version is fine with this function. On Wed, Mar 24, 2010 at 12:27 PM, zrl wrote: > Dear list, > > After asking how to do cross specices annotation. I tried BiomaRt, and > find there is direct function "getHomolog" describe ...
written 9.5 years ago by Roger Liu260
0
votes
3
answers
753
views
3
answers
where is the "getHomolog" function in biomaRt?
... Dear list, After asking how to do cross specices annotation. I tried BiomaRt, and find there is direct function "getHomolog" described in its manual to do this. But when I try to use it, it gave me the error: "Error: could not find function "getHomolog" Could anyone explain this to me? where sho ...
annotation biomart written 9.5 years ago by Roger Liu260 • updated 9.5 years ago by Wolfgang Huber13k
0
votes
2
answers
656
views
2
answers
Comment: C: how to do cross species annotation?
... Thank you Michael, that's a very straightforward way to do it. Alexandre aslo provide an more direct way to do it. -Qiudao On Wed, Mar 24, 2010 at 10:03 AM, michael watson (IAH-C) wrote: > I'd use biomaRt > > 3 queries: > > Affy human to human ensembl id > Human ensemble id to m ...
written 9.5 years ago by Roger Liu260
0
votes
2
answers
656
views
2
answers
Comment: C: how to do cross species annotation?
... Thanks. Alexandre. That's the tool I am looking for. I thought I saw that before, just forget its names. Qiudao. On Wed, Mar 24, 2010 at 10:38 AM, Alexandre Kuhn wrote: > Quidao, > you can check the package annotationTools > (http://www.bioconductor.org/packages/release/bioc/html/annotat ...
written 9.5 years ago by Roger Liu260
0
votes
2
answers
656
views
2
answers
how to do cross species annotation?
... Dear list, If I have a set of affy probes (probe sets) from Human platform, and I want identify the corresponding probes (probe sets) in mouse platform, vice versa. Is there a tool/package to do that? Thanks. Qiudao ...
affy written 9.5 years ago by Roger Liu260 • updated 9.5 years ago by Alexandre Kuhn60
0
votes
1
answer
771
views
1
answers
Comment: C: GSEA using Broad genesets
... Thank you Martin. If we caculate the statistic in each gene set,is it possible that several probes mapped to the same gene. How will GSEABase deal with the calculation of statistic of a gene set with multiple probes mapped to the same gene? (or maybe this quesiton should be directed to using "catego ...
written 9.6 years ago by Roger Liu260
0
votes
1
answer
771
views
1
answers
Comment: C: GSEA using Broad genesets
... Thank you Martin, these are what I want. I like the second method to create incidence matrix. My last question is in GSEABase when we do this: "gsc <- GeneSetCollection(bcrneg_filt1, setType=KEGGCollection())" how does GSEABase collapse the affy probes to gene symbols? (max,mean,median or not a ...
written 9.6 years ago by Roger Liu260
0
votes
1
answer
771
views
1
answers
Comment: C: GSEA using Broad genesets
... Hi Martin, Thank you for answering my question. Sorry I didn't make my question clearly. In the case of "gsc <- GeneSetCollection(bcrneg_filt1, setType=KEGGCollection())" and "Am<-incidence(gsc)", we use KEGG as reference to create gene sets of bcrneg_filt1, then create a incidence. My quest ...
written 9.6 years ago by Roger Liu260
0
votes
1
answer
771
views
1
answer
GSEA using Broad genesets
... Dear list, I have a question regarding using broad gene sets for GSEA anlaysis. As we know, we have "gsc <- GeneSetCollection(bcrneg_filt1, setType=KEGGCollection())" and "Am<-incidence(gsc)" to generate incidence matrix for further anlaysis. I have learned to get the geneset file from Broa ...
written 9.6 years ago by Roger Liu260 • updated 9.6 years ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
631
views
1
answers
Comment: C: question regarding genefilter package
... Thank you Jim. I think you pretty much answered my questions. So, the "var.cutoff" is actually the quantile of the IQRs calculated of all the rows/genes. Do I understand this right? Thanks. Qiudao. On Tue, Feb 2, 2010 at 2:28 PM, James W. MacDonald wrote: > Hi Whomever, > > zrl wrote: & ...
written 9.6 years ago by Roger Liu260

Latest awards to Roger Liu

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 300 users visited in the last hour