User: glocke01

gravatar for glocke01
glocke01170
Reputation:
170
Status:
Trusted
Location:
United States
Last seen:
9 months, 4 weeks ago
Joined:
8 years, 1 month ago
Email:
g*******@gmail.com

about me

Posts by glocke01

<prev • 28 results • page 1 of 3 • next >
0
votes
2
answers
3.4k
views
2
answers
Comment: C: Download all DNA mutations from TCGA
... try https://portal.gdc.cancer.gov/repository ...
written 13 months ago by glocke01170
0
votes
1
answer
543
views
1
answers
Comment: C: how do I properly use edgeR::scaleOffset to combine two targeted RNA-seq panels?
... thanks once again, Prof. Smyth!! ...
written 14 months ago by glocke01170
0
votes
1
answer
381
views
1
answers
Comment: C: differential gene set testing combining genes from multiple panels
... Thanks again, Gordon. I'm not sure that I'm using `scaleOffset` correctly, and I've asked another question requesting further assistance. https://www.biostars.org/p/370793/ Any help from you or Aaron or anyone would be great. ...
written 14 months ago by glocke01170
3
votes
1
answer
543
views
1
answer
how do I properly use edgeR::scaleOffset to combine two targeted RNA-seq panels?
... I am trying to analyze some targeted RNA-seq data, where for each sample/mouse I have data from two panels. Because there are two panels, the data for each sample effectively have two library sizes. This means I can't just rbind the two panels together and use a normal RNA seq workflow. In principle ...
panel rna-seq edger written 14 months ago by glocke01170
0
votes
1
answer
381
views
1
answers
Comment: C: differential gene set testing combining genes from multiple panels
... awesome, thanks!! ...
written 14 months ago by glocke01170
2
votes
1
answer
381
views
1
answer
differential gene set testing combining genes from multiple panels
... I have RNA-seq data from two targeted panels. So, for each sample/mouse, I have one counts matrix for one set of genes, and another matrix for another set of genes. The major problem here is that the library size for a given sample is different across the two panels, so just slapping the two matrice ...
pathway limma rna-seq voom written 14 months ago by glocke01170 • updated 14 months ago by Gordon Smyth1.6k
0
votes
2
answers
681
views
2
answers
Comment: C: GSEA top genes vs all platform
... You can also use gene set tests included in the limma package, i.e. CAMERA and ROAST. CAMERA, in particular, is way, way faster than GSEA. Prof. Smyth has made the MSigDB gene sets available in easy to ingest .rda files at his website: http://bioinf.wehi.edu.au/software/MSigDB/index.html ...
written 22 months ago by glocke01170
0
votes
1
answer
477
views
1
answers
Comment: C: Pathway test for reversal of effect (three-condition comparison)
... I think a geometric/harmonic average might be appropriate (as opposed to the arithmetic mean implicit in my SNR statistic) so that small values in either comparison would strongly penalize the final statistic... ...
written 22 months ago by glocke01170
0
votes
1
answer
477
views
1
answers
Comment: C: Pathway test for reversal of effect (three-condition comparison)
... Nice. Good thinking: rank based on some relevant comparison, send ranks to GSEA or suchlike. I guess the trouble is defining a single number for ranking purposes - by signal to noise, I take it you're thinking something like `(mean in A minus mean in AB and ∅)/stdev(all samples)`. Something like av ...
written 22 months ago by glocke01170
0
votes
1
answer
477
views
1
answers
Comment: C: Pathway test for reversal of effect (three-condition comparison)
... It's relatively simple to describe what I'm looking for as "effects of `A` reversed by `B`", but I am aware that that language is substantively imprecise - literal reversal would be treating with `A` then `B`. The biological question of interest would be more accurately described as "effects of `A - ...
written 22 months ago by glocke01170

Latest awards to glocke01

Great Question 15 months ago, created a question with more than 5,000 views. For How can I shuffle a set of sequences while preserving the dinucleotide distribution?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Changes to dispersion estimates in DESeq2?
Supporter 2.7 years ago, voted at least 25 times.
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Changes to dispersion estimates in DESeq2?
Scholar 4.3 years ago, created an answer that has been accepted. For A: How Can I Apply A Pssm Efficiently?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For How Can I Apply A Pssm Efficiently?
Student 5.0 years ago, asked a question with at least 3 up-votes. For How can I shuffle a set of sequences while preserving the dinucleotide distribution?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For How Can I Apply A Pssm Efficiently?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1160 users visited in the last hour