User: siajunren

gravatar for siajunren
siajunren0
Reputation:
0
Status:
New User
Last seen:
1 month, 3 weeks ago
Joined:
2 years, 7 months ago
Email:
s********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by siajunren

<prev • 13 results • page 1 of 2 • next >
0
votes
1
answer
226
views
1
answers
Comment: C: numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
... Just beautiful.I didn't know there's a GOALL keytype. ...
written 12 months ago by siajunren0
3
votes
1
answer
226
views
1
answer
numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
... Hi, The number of genes in a GO geneset determined by goseq is different from what I obtained by querying org.Hs.eg.db. I ran the following: library(goseq) data(genes) pwf.eg=nullp(genes,"hg19","ensGene") GO.wall.eg=goseq(pwf.eg,"hg19","ensGene", test.cats='GO:BP') head(GO.wall.eg,5) It shows t ...
goseq written 12 months ago by siajunren0 • updated 12 months ago by James W. MacDonald50k
0
votes
1
answer
216
views
1
answers
Comment: C: Is number of rotations dependent on number of gene sets in mroast?
... That's true, didn't consider that. Thanks. I indeed was asking a much more basic question. ...
written 12 months ago by siajunren0
0
votes
1
answer
191
views
1
answers
Comment: C: Conditions for using Fry
... I checked and found my df.prior to be 12.21. Would you consider that to be sufficiently large for fry to be a good approximation? ...
written 12 months ago by siajunren0
3
votes
1
answer
216
views
1
answer
Is number of rotations dependent on number of gene sets in mroast?
... When testing more gene sets with mroast, should number of rotations be increased to maintain the accuracy of p values? If I use x number of rotations for testing 1 gene set, should I use perhaps 10x number of rotations for 10 gene sets so that each gene set gets x rotations? This question obviously ...
limma mroast written 12 months ago by siajunren0 • updated 12 months ago by Gordon Smyth38k
3
votes
1
answer
191
views
1
answer
Conditions for using Fry
... What conditions should be fulfilled for Fry to be a good approximation of mroast with infinite rotations? The manual says that the df.prior should be large and set.statistic="mean". What determines the prior degree of freedom of residual variance? I am guessing it is the number of replicates per exp ...
limma mroast fry written 12 months ago by siajunren0 • updated 12 months ago by Gordon Smyth38k
0
votes
1
answer
2.2k
views
1
answers
Comment: C: limma roast syntax and interpretation
... For the last line of your code: roast(e, myIndex, design, contrasts=cont.matrix, nrot=5000) Shouldn't it be "contrast" instead of "contrasts"? And shouldn't the argument be a numerical vector corresponding to the columns of the design matrix instead of a full contrast matrix? ...
written 12 months ago by siajunren0
2
votes
1
answer
1.4k
views
1
answer
Intepretation of Z scores for gene set enrichment analysis in MAST
... I performed zlmfit on a matrix with MAST for 2 populations of cells, A and B, with population A as intercept. Then I run gseaAfterBoot on the zlfit object after performing bootstrapping with bootVcov1. If I get a positive value Z score for a particular gene set, does it mean that genes in this genes ...
gsea scrna mast written 2.1 years ago by siajunren0 • updated 2.1 years ago by Andrew_McDavid190
0
votes
2
answers
965
views
2
answers
How does newSCESet calculate expression matrix
... In the Scater package, according to the vignette, newSCESet generates the exprs slot as log2(counts-per-million) using the cpm function from edgeR, with a “prior count” value of 1. However, this is not the case when I checked. library(scater) set.seed(221) y <- matrix(rnbinom(20,size=1,mu=10),5 ...
scater written 2.2 years ago by siajunren0 • updated 2.2 years ago by davis90
0
votes
1
answer
437
views
1
answers
Comment: C: calcAverage missing from Scater package
... After updating my R to the latest version, I could run the calcAverage now. Thank you. ...
written 2.2 years ago by siajunren0

Latest awards to siajunren

Popular Question 12 months ago, created a question with more than 1,000 views. For Intepretation of Z scores for gene set enrichment analysis in MAST

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 138 users visited in the last hour