Moderator: Michael Love

gravatar for Michael Love
Michael Love12k
Reputation:
11,620
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
10 hours ago
Joined:
4 years, 2 months ago
Email:
m****************@gmail.com

Michael I. Love, Dr. rer. nat.
Assistant Professor
Departments of Biostatistics and Genetics
University of North Carolina-Chapel Hill

My main Bioconductor involvement is to maintain these software packages

and the RNA-seq gene-level workflow.

Posts by Michael Love

<prev • 2,194 results • page 1 of 220 • next >
0
votes
1
answers
25
views
1
answers
Answer: A: DESeq2 ddsHTSeq error
... The test that's failing is one which checks that the first column is identical for all files. So can you do some more spot testing on your end? ...
written 10 hours ago by Michael Love12k
0
votes
1
answers
70
views
1
answers
Comment: C: DESeq2- what to do when two conditions share controls?
... I just updated my answer below, because I think you also need estrogen (you are assuming different slopes according to the introduction of estrogen?) I'll have to answer the rest of your questions later. ...
written 16 hours ago by Michael Love12k
0
votes
1
answers
70
views
1
answers
Answer: A: DESeq2- what to do when two conditions share controls?
... hi Rachel, You can code the control samples as "Tam", and then use a design that doesn't have a difference between PFOA and Tam at concentration=0. This is saying that at concentration=0, the expected expression for two chemicals are equal (i.e. control). It would look like a design of ~rep + estro ...
written 18 hours ago by Michael Love12k
0
votes
1
answers
45
views
1
answers
Answer: A: deseq2 course experiment
... Check the vignette section on interactions, there is a diagram of how interaction terms work. This is the 30 vs 0 difference for WT, the mut vs WT difference at time 0, and the interaction for mut and time 15.     ...
written 22 hours ago by Michael Love12k
0
votes
1
answers
33
views
1
answers
Answer: A: DESeq2: Tests of log2 differences
... Does this answer?  https://support.bioconductor.org/p/61509/     ...
written 1 day ago by Michael Love12k
0
votes
1
answers
70
views
1
answers
Comment: C: DESeq2- what to do when two conditions share controls?
... Is a technical replicate here just more sequencing of the same library? I would collapse these into a single count. So that would reduce your rows down by a factor of 3. We have a function in DESeq2 to do this, but I want to make sure that I get it right. And so PL1A_B02, PL1A_C02, and PL1A_D02 are ...
written 1 day ago by Michael Love12k
0
votes
1
answers
70
views
1
answers
Comment: C: DESeq2- what to do when two conditions share controls?
... Is there more experimental information missing? Are the 'B' samples related? Where is the presence/absence of estrogen? ...
written 1 day ago by Michael Love12k
0
votes
1
answers
46
views
1
answers
Comment: C: DESeq2 minReplicatesForReplace with different group size
... If you don't see extreme outliers (what I mean by this is, e.g. 3 samples with single digit counts and 1 sample with a count of 1000+), then I would continue with the default (where outliers are only replaced among the 14). Re: my comment which you didn't catch, if you don't see outliers in the gene ...
written 1 day ago by Michael Love12k
0
votes
1
answers
70
views
1
answers
Comment: C: DESeq2- what to do when two conditions share controls?
... Can you post the colData (the table where columns are variables and rows are samples). This makes it much easier to understand the design. You can do as.data.frame(colData(dds)) ...
written 1 day ago by Michael Love12k
0
votes
1
answers
32
views
1
answers
Answer: A: DESeq2 rlogTransformation error
... You can check over the workflow: http://www.bioconductor.org/help/workflows/rnaseqGene/#the-rlog-and-variance-stabilizing-transformations Note that, in the workflow, we call rlog() on a 'dds' object, like so: rld <- rlog(dds) Above you are calling the function on a matrix. rlog() will take c ...
written 1 day ago by Michael Love12k

Latest awards to Michael Love

Good Answer 6 days ago, created an answer that was upvoted at least 5 times. For A: DESeq2 Model Design
Scholar 7 days ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Scholar 10 days ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Popular Question 13 days ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Popular Question 14 days ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Appreciated 20 days ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 21 days ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 5 weeks ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Appreciated 6 weeks ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 6 weeks ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 7 weeks ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Appreciated 8 weeks ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 11 weeks ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 paired multifactor test
Scholar 11 weeks ago, created an answer that has been accepted. For A: trouble installing DESeq2
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 11 weeks ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 221 users visited in the last hour