The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor
User: JMallory
JMallory • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 1 year, 1 month ago
- Joined:
- 1 year, 7 months ago
- Email:
- t******@uci.edu
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by JMallory
<prev
• 7 results •
page 1 of 1 •
next >
0
votes
1
answer
277
views
1
answer
... Hi,
I have a list of DE transcripts emerging from an analysis of RNA-seq data. I have mapped these transcripts back to their Ensembl ENSG IDs for submission to the `findMotifs.pl` function in the `HOMER` software suite http://homer.ucsd.edu/homer/microarray/index.html.
As described by the link, ...
written 13 months ago by
JMallory • 0
• updated
13 months ago by
Ou, Jianhong • 1.1k
0
votes
1
answer
1.1k
views
1
answers
... Spot on. Thanks very much James.
...
written 15 months ago by
JMallory • 0
1
vote
1
answer
1.1k
views
1
answer
... I have successfully conducted a gene ontology analysis using goseq. In presenting the findings of the analysis (i.e., the standard output generated by the `goseq` function) to a colleague, he quite reasonably asked which genes present in the vector passed to the `pwf` function were those associated ...
written 15 months ago by
JMallory • 0
• updated
15 months ago by
James W. MacDonald ♦ 49k
0
votes
1
answer
361
views
1
answers
... I see. Yes, I have multiple transcripts/splice variants of a single gene mapping to a single Entrez ID in my user data. If I am understanding correctly, this is the source of the issue. The algorithm is simply selecting the first fold change value associated with a given gene ID for use in further c ...
written 16 months ago by
JMallory • 0
0
votes
3
answers
421
views
3
answers
... Peter, I have used WGCNA in the past, but was unaware of this function. As per its description in the documentation, it does exactly what I have been trying to get at for the past few weeks. Criminally underappreciated bit of code. Thank you.
...
written 16 months ago by
JMallory • 0
2
votes
3
answers
421
views
3
answers
... Is there a way to use ComBat to return a data matrix adjusted by only numeric covariates? As implemented in SVA, ComBat allows for adjustment of data by numeric covariates, but only if a batch effect (i.e., a factor variable) is also provided. What if I just want to "clean" a data matrix of several ...
written 16 months ago by
JMallory • 0
• updated
16 months ago by
W. Evan Johnson • 790
1
vote
1
answer
361
views
1
answer
... I have been using the following tutorial by Stephen Turner and Will Bush to look at some RNA-seq data.
http://www.gettinggeneticsdone.com/2015/12/tutorial-rna-seq-differential.html
Looking into GAGE's documentation, it looks like this tutorial is using it in a somewhat non-standard way. Specifica ...
written 16 months ago by
JMallory • 0
• updated
16 months ago by
Luo Weijun • 1.4k
Latest awards to JMallory
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 259 users visited in the last hour