Moderator: Michael Love

gravatar for Michael Love
Michael Love13k
Reputation:
13,270
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
16 minutes ago
Joined:
4 years, 6 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 • 2,576 results • page 1 of 258 • next >
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... Another comment, we do reference, in DESeq2 Methods section, microarray methods which proposed moderated fold changes, e.g. Newton et al 2001. This section starts with: "As was observed with differential expression analysis using microarrays, genes with low intensity values tend to suffer from a sma ...
written 1 hour ago by Michael Love13k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... This isn't so much an answer, but a comment. While I of course think a Bayesian posterior LFC is a useful statistic, it's not straightforward to implement. Figuring out an algorithm to output a reasonable scale of the prior is not trivial. The shrinkage estimator for DESeq2 is always biased toward 0 ...
written 3 hours ago by Michael Love13k
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Answer: A: DESeq2 Which gene used to normalize?
... hi, Take a look at the original DESeq paper. DESeq2 uses the median ratio method described here for normalization. The default normalization is the estimation of size factors presented in Equation 5. The default size factor estimate uses all of the genes that have positive counts for all samples. ...
written 8 hours ago by Michael Love13k
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Answer: A: DESeq2 Dispersion Shrinkage - more samples is better?
... These are good questions. Let me start with the question about the mean of the dispersion prior. In the DESeq2 paper we assume a prior on the dispersion parameter which is dependent on the mean of normalized counts for a gene, so we write alpha_tr(mu-bar), where the 'tr' stands for 'trend'. The func ...
written 1 day ago by Michael Love13k
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Answer: A: Different PCA plots using rlog and vsd on the same data set
... Can you describe the data or the plots? How large of differences, experimental design, etc. There is some description of differences in the vignette. ...
written 1 day ago by Michael Love13k
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Comment: C: Obtaining transcript names in RSEM
... Instead of changing the column names, you should use the tximport arguments: geneIdCol, txIdCol, abundanceCol, countsCol, and lengthCol. If txOut=TRUE, then geneIdCol will be ignored so you can put anything. We only are currently supporting RSEM's gene-level counts with type="RSEM". It would take m ...
written 2 days ago by Michael Love13k
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Comment: C: Obtaining transcript names in RSEM
... You can do whatever you like with the quantifications. Variance stabilization is a good idea for calculating sample distances or ordination plots like PCA or MDS. You can read in the matrix from the isoforms table using base R functions for RSEM, and txOut with tximport. ...
written 2 days ago by Michael Love13k
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Answer: A: Obtaining transcript names in RSEM
... The tximport to DESeq2 pipeline described in the tximport vignette is designed for gene level analysis. ...
written 2 days ago by Michael Love13k
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Comment: C: Sample-to-sample distance matrix using heatmap.2
... If you see my code below, I am plotting the correlation [-1,1] and the clustering distances are specified as dist(x,y) = 1-cor(x,y).  From our workflow: In order to plot the sample distance matrix with the rows/columns arranged by the distances in our distance matrix, we manually provide sampleDis ...
written 3 days ago by Michael Love13k
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Comment: C: problem with DESeq2 on metagenome analysis
... Yes, and you can visualize the differences with PCA. The choice whether to run all together or in separate batches is up to you, and should be guided by these pieces of evidence. ...
written 3 days ago by Michael Love13k

Latest awards to Michael Love

Scholar 3 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 3 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 3 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 3 months ago, asked a question with at least 3 up-votes. For recount counts in the example experiment
Appreciated 3 months ago, created a post with more than 5 votes. For A: DESeq2 Model Design
Scholar 3 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 3 months ago, asked a question with at least 3 up-votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 Model Design
Scholar 4 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 4 months 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 4 months 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 4 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 4 months 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 4 months 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 4 months ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Popular Question 4 months ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Appreciated 4 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 4 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 5 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 5 months 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 5 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 5 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 5 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Appreciated 6 months ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)

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