User: CPR

gravatar for CPR
CPR30
Reputation:
30
Status:
New User
Location:
Chicago
Scholar ID:
Google Scholar Page
Last seen:
3 years, 2 months ago
Joined:
3 years, 4 months ago
Email:
C**@u.northwestern.edu

Posts by CPR

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
3.6k
views
1
answers
Comment: C: limma lmFit coefficients and p-values
... Ok great that's very helpful. This is my first go at DMR analysis and so will try a few different approaches and try to figure out what the consensus is as to the 'best' one. Hopefully I can avoid the 'false' degrees of freedom issue Steve and yourself reminded me about when 'correcting', possibly ...
written 3.2 years ago by CPR30
0
votes
1
answer
3.6k
views
1
answers
Comment: C: limma lmFit coefficients and p-values
... Ok awesome that makes sense, thanks @Ryan C. Thompson! ...
written 3.3 years ago by CPR30
0
votes
1
answer
3.6k
views
1
answers
Comment: C: limma lmFit coefficients and p-values
... Thanks for your help and patience Steve. That makes a lot of sense about using ALL probes for eBayes(.). I'll make sure to keep that in mind from now on, and try the approaches (subset 'fit' or readjust p-values) you described. With respect to the DMR analysis I mentioned, I'll clarify: In another ...
written 3.3 years ago by CPR30
0
votes
1
answer
3.6k
views
1
answers
Comment: C: limma lmFit coefficients and p-values
... Right, coef(2) was a syntax error for coef = 2, my apologies. Where I'm struggling a bit is that you say coef = 2 is not equivalent to coef = c(1, 2). Why? Isn't a two level factor always compared to the value of the intercept in a way? So in summary(lm(model) the intercept will be for one of the t ...
written 3.3 years ago by CPR30
0
votes
1
answer
3.6k
views
1
answers
Comment: C: limma lmFit coefficients and p-values
... That's so much @Steve Lianoglou for such a prompt and thorough response! My query is on an a priori set subset of candidate genes (~250 CpG probes total), so I only ran the lmFit for those probes. Fairly straightforward there. In some cases I'm also running a DMR analysis after the lmFit, which re ...
written 3.3 years ago by CPR30
14
votes
1
answer
3.6k
views
6 follow
1
answer
limma lmFit coefficients and p-values
... I'm running a series of linear regressions on a subset of candidate genes using lmFit(.) from the limma package. Two, hopefully simple questions: 1. I am trying to create a matrix of residuals controlling for another factor (sex) so I can look at the effects of a series of variables in a loop. Does ...
limma methylation ewas written 3.3 years ago by CPR30 • updated 3.3 years ago by Steve Lianoglou12k
0
votes
1
answer
808
views
1
answers
Answer: A: Unable to load any IlluminaHumanMethylation450k annotation
... I found what turned out to be a relatively simple solution: I removed "Genomic Ranges" package, closed and quit R. I then re-opened R, and ran: library("FDb.InfiniumMethylation.hg19"). It installed, but I got the error: Error: package ‘GenomicRanges’ required by ‘GenomicFeatures’ could not be f ...
written 3.3 years ago by CPR30
0
votes
1
answer
808
views
1
answer
Unable to load any IlluminaHumanMethylation450k annotation
... Dear Bioconductors, I've been trying to set up data to run a DMR analysis for the Illumina Infinium HumanMethylation450. I have a matrix of probes and individual human id's, but I need to merge these with probe specific data, especially location data for the DMR analysis (seqLM, but still learning ...

Latest awards to CPR

Popular Question 3.2 years ago, created a question with more than 1,000 views. For limma lmFit coefficients and p-values

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 432 users visited in the last hour