User: brhead

gravatar for brhead
brhead30
Reputation:
30
Status:
New User
Location:
Last seen:
1 year, 10 months ago
Joined:
2 years, 10 months ago
Email:
b*****@gmail.com

Posts by brhead

<prev • 12 results • page 1 of 2 • next >
0
votes
0
answers
1.3k
views
0
answers
Comment: C: Difference between "be" and "leek" methods when deciding number of surrogate var
... Hi Srikant, Sorry I didn't see your message earlier! I found this paper to be helpful in deciding what to do: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0808-5 As the article points out, a large number of surrogate variables may be capturing more than you intend. Plus ...
written 2.1 years ago by brhead30
3
votes
0
answers
1.3k
views
0
answers
Difference between "be" and "leek" methods when deciding number of surrogate variables to estimate with SVA?
... I am trying to estimate sources of heterogeneity in methylation data in addition to some known sources (i.e., I have batch and age but would also like to correct for smoking, unmeasured technical artifacts, and cellular heterogeneity). When I use num.sv and the default "be" method, I get 12 SVs; whe ...
sva num.sv written 2.3 years ago by brhead30
0
votes
1
answer
1.2k
views
1
answers
Comment: C: difference in detection p-values from Minfi vs. GenomeStudio
... Great! I just sent you an email. Let me know if you need anything else. -Brooke ...
written 2.4 years ago by brhead30
0
votes
1
answer
1.2k
views
1
answers
Comment: C: difference in detection p-values from Minfi vs. GenomeStudio
... Thanks, Kasper! Here is the documentation that Illumina tech support pointed me to: "The information we have on the algorithms used in GenomeStudio Methylation are found in the user guide, linked here: https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_docume ...
written 2.4 years ago by brhead30
0
votes
1
answer
1.1k
views
1
answers
Comment: C: goseq ERROR: SupportedOrganisms() subscript out of bounds
... This solved my problem... thanks! ...
written 2.4 years ago by brhead30
0
votes
1
answer
1.2k
views
1
answers
Comment: C: difference in detection p-values from Minfi vs. GenomeStudio
... Thank you for the fast and helpful response, James. I also contacted Illumina tech support and they basically said the same thing -- that they are using a different algorithm to generate detection p values. ...
written 2.4 years ago by brhead30
0
votes
1
answer
1.2k
views
1
answer
difference in detection p-values from Minfi vs. GenomeStudio
... I am using Minfi to process data from Illumina EPIC methylation beadChips and I have found a discrepancy between the number of CpGs that GenomeStudio reports with a detection P value <0.01 and the number that I get reading in the .idat files using Minfi in R. For example, in a recent batch I had ...
minfi methylation genomestudio written 2.4 years ago by brhead30 • updated 2.4 years ago by James W. MacDonald51k
0
votes
1
answer
1.4k
views
1
answers
Comment: C: bumphunter output clarification
... That clears it up! Thank you! ...
written 2.8 years ago by brhead30
0
votes
1
answer
1.4k
views
1
answers
Comment: C: bumphunter output clarification
... This is helpful! Can anyone clarify what the difference is between the region and the cluster on this bit?: L - is the number of probes in the region clusterL - number of probes in the cluster   ...
written 2.8 years ago by brhead30
0
votes
1
answer
1.0k
views
1
answers
Comment: C: Using Bumphunter and SVA together in Minfi: bumphunterEngine nullMethod warning
... Dear James, Thank you for all of your help with my bumphunter questions. I was able to solve the "Inf" problem . . . it turns out that there were ~100 infinite M values in my matrix. I'm not sure why they were there, but once I removed them, bumphunter stopped producing "Inf" and "-Inf" values in t ...
written 2.8 years ago by brhead30

Latest awards to brhead

Popular Question 22 months ago, created a question with more than 1,000 views. For difference in detection p-values from Minfi vs. GenomeStudio

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 434 users visited in the last hour