User: rmccloskey

gravatar for rmccloskey
rmccloskey180
Reputation:
180
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Trusted
Location:
Canada
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Last seen:
2 years, 6 months ago
Joined:
3 years, 10 months ago
Email:
r************@gmail.com

M.Sc. Bioinformatics Candidate, Bioinformatics Training Program, University of British Columbia

B.Sc. Mathematics, Simon Fraser University

Posts by rmccloskey

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Is there an informative subset of 450k methylation probes?
... I have 389 samples. I agree that it's best to use as much information as possible, but I'm already running on a cluster and am still having memory issues. ...
written 3.3 years ago by rmccloskey180
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Is there an informative subset of 450k methylation probes?
... I'm working on an analysis which includes 450k methylation data. There are so many probes that analysing the whole data set is becoming a problem in terms of time and memory. I'm sure that nearby methylation sites are highly correlated, so is there some kind of informative subset of the whole probse ...
450k illumina methylation written 3.3 years ago by rmccloskey180 • updated 3.3 years ago by Charles Warden5.1k
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Answer: A: Ancestral Sequence Reconstruction from Multiple Sequence Alignment using Mesquit
... As far as I know, Mesquite has support only to reconstruct a single discrete state at a time. So if you want to reconstruct the entire ancestral sequence, you would have to encode each position as a separate state (like the categorical example data), then reconstruct them all separately. Obviously t ...
written 3.4 years ago by rmccloskey180
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Comment: C: Why use the qvalue package instead of p.adjust in R stats?
... Thanks for the great explanation! ...
written 3.5 years ago by rmccloskey180
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Why use the qvalue package instead of p.adjust in R stats?
... A lot of papers I've read have used the qvalue package from Bioconductor to do multiple testing correction. There is a function in the basic R stats package called p.adjust which seems to do the same thing. What is the advantage of the qvalue package, and why is it so frequently used instead of the ...
R qvalue written 3.5 years ago by rmccloskey180 • updated 3.5 years ago by Devon Ryan81k
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Illumina 450K array manifest for hg38?
... I'm looking to map the results of some methylation experiments, performed with the Illumina 450K array, to hg38. I know there is a manifest on Illumina's website as well as in UCSC, but those are for hg19. Is there a source for the locations of the CpG probes on hg19, or should I just liftOver from ...
450k illumina hg38 methylation written 3.5 years ago by rmccloskey180
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Comment: C: How to edit flags in a BAM file?
... Oops! Sorry, I did a bunch of searching but failed to find that answer. Thanks! ...
written 3.9 years ago by rmccloskey180
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(Closed) How to edit flags in a BAM file?
... I have a number of BAM files with a very high number of reads flagged as duplicates (>50%). To confirm that these are indeed duplicates and the flags were not introduced erroneously during processing, I would like to clear all the duplicate read flags and run Picard tools MarkDuplicates to rechec ...
bam samtools written 3.9 years ago by rmccloskey180

Latest awards to rmccloskey

Appreciated 3.3 years ago, created a post with more than 5 votes. For Why use the qvalue package instead of p.adjust in R stats?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Why use the qvalue package instead of p.adjust in R stats?
Student 3.3 years ago, asked a question with at least 3 up-votes. For Illumina 450K array manifest for hg38?
Student 3.5 years ago, asked a question with at least 3 up-votes. For Why use the qvalue package instead of p.adjust in R stats?
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

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