User: Michael Love

gravatar for Michael Love
Michael Love1.9k
Reputation:
1,930
Status:
Trusted
Location:
United States
Website:
https://twitter.com/mi...
Scholar ID:
Google Scholar Page
Last seen:
1 month, 2 weeks ago
Joined:
5 years, 11 months ago
Email:
m****************@gmail.com

Posts by Michael Love

<prev • 102 results • page 1 of 11 • next >
1
vote
0
answers
183
views
0
answers
Comment: C: Is a simple Wilcoxon rank sum test good enough to identify differentially expres
... I agree with Devon here except I'd put the number even lower than 100 for trusting Wilcoxon. Rank based tests will find differences with sufficient power once you have, say dozens of cells with non-zero counts in each group that you want to compare. We used Wilcoxon tests with Gibbs samples to also ...
written 7 weeks ago by Michael Love1.9k
0
votes
1
answer
417
views
1
answers
Comment: C: model design in rna seq - deseq2
... Cross posted to Bioconductor https://support.bioconductor.org/p/119352/ ...
written 12 months ago by Michael Love1.9k
2
votes
1
answer
5.8k
views
1
answers
Comment: C: How is the design in DESeq2 work?
... Just posted this on twitter, but cross-posting here too: The syntax is originally from here: https://www.jstor.org/stable/2346786?seq=1#metadata_info_tab_contents It is sometimes called Wilkinson (& Rogers) syntax. In the vignette, there are diagrams on interpreting [interactions][1]. A brief ...
written 16 months ago by Michael Love1.9k
0
votes
1
answer
1.0k
views
1
answers
Comment: C: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
... Please note the cross post on both sites: https://support.bioconductor.org/p/115065/ ...
written 16 months ago by Michael Love1.9k
1
vote
1
answer
2.9k
views
1
answers
Answer: A: "Duplicate rownames not allowed" when the rownames are not duplicated
... To propagate the answer from Bioconductor support site back here: > The problem is that you have duplicate columns of colData(dds), which > breaks some code where replaceOutliers adds a column to colData(dds) > and adds some metadata about that column. > > `sum(duplicated(colnames(c ...
written 17 months ago by Michael Love1.9k
0
votes
0
answers
1.9k
views
0
answers
Comment: C: Deseq2 question of a single factor with 3 levels
... This post was cross posted at Bioconductor which means volunteers have to answer a question twice. https://www.biostars.org/p/294625/ ...
written 2.2 years ago by Michael Love1.9k
1
vote
0
answers
1.3k
views
0
answers
Comment: C: Changes log2FC values of DESeq2
... This is likely it. You can look for descriptions of important user relevant changes to R packages in the NEWS file. Also, here’s a longer post on motivation for the change. https://support.bioconductor.org/p/95695/ ...
written 2.3 years ago by Michael Love1.9k
7
votes
1
answer
1.8k
views
1
answers
Answer: A: How to import RSEM results to DESeq2 for differential analysis
... You can use tximport to import RSEM quants and then `DESeqDataSetFromTximport()` in DESeq2. The development version of tximport allows importing transcript-level abundances as well (previously just gene-level). ---------- Edit 4.3.2020 by https://www.biostars.org/u/25721/ since this thread gets ...
written 2.3 years ago by Michael Love1.9k • updated 4 weeks ago by ATpoint32k
2
votes
4
answers
14k
views
4
answers
Comment: C: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
... p-values are indeed hard for many to interpret. Also, for many genomics datasets, the point null of no change is trivial to reject. We try to move towards working more directly with posterior estimates of the effect size itself. ...
written 2.4 years ago by Michael Love1.9k
0
votes
0
answers
1.2k
views
0
answers
Comment: C: Strange distribution of logFC
... Cross-posting is discouraged as you are asking for duplicate effort from the volunteers who answer: https://support.bioconductor.org/p/102905/ ...
written 2.4 years ago by Michael Love1.9k

Latest awards to Michael Love

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 12 months ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: What exactly means the Dispersion Plot DESeq2?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 15 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Appreciated 16 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Centurion 16 months ago, created 100 posts.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: What exactly means the Dispersion Plot DESeq2?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.5 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Popular Question 3.0 years ago, created a question with more than 1,000 views. For New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: What exactly means the Dispersion Plot DESeq2?
Supporter 3.7 years ago, voted at least 25 times.
Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Can someone please explain in simple terms how DESeq2 works?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1876 users visited in the last hour