Moderator: Michael Love

gravatar for Michael Love
Michael Love17k
Reputation:
16,720
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
5 years, 1 month 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 • 3,389 results • page 1 of 339 • next >
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Answer: A: processing of (salmon) gene counts for eqtl analysis
... "Do the two methods work in a similar way, and can either be applied to edgeR/DESeq2/limma-voom?" This is covered in that section of the tximport vignette, but I can review: You can use edgeR and DESeq2 with the counts plus an offset, OR you can use the countsFromAbundance technique and pass the " ...
written 9 hours ago by Michael Love17k
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Answer: A: Differentially expressed genes detection between three classes with a batch effe
... If you want log2 fold changes from the original object you can just use "name" to specify which LFC to extract. See the LRT section of ?results. E.g.: results(dds, name="condition_C_vs_A") results(dds, name="condition_B_vs_A") If dds involved an LRT, then the p-values won't change between these t ...
written 10 hours ago by Michael Love17k
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Comment: C: Results counts post DESeq same raw counts
... Yes plotCounts does this, see ?plotCounts or look at the y axis label in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#plot-counts ...
written 14 hours ago by Michael Love17k
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Answer: A: Results counts post DESeq same raw counts
... hi, A quick answer to this one: "However, I have noticed that the count matrix I am making post DESeq on significantly expressed genes are actually exactly the same as the initial raw counts table..." DESeq2 models the raw counts, while using size factors or normalization factors to account for d ...
written 16 hours ago by Michael Love17k
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Answer: A: DESeq2 with multi level
... The first time you call lfcShrink, you are giving the software conflicting information. You are saying to shrink coef=2, which refers to "condition_K_I50_vs_K_DMSO" (the second element of resultsNames(dds)), but you are supplying the results table "resM_5000vsM_DMSO", which describes a different com ...
written 1 day ago by Michael Love17k
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Comment: C: DESeq2 with multi level
... Oops, I missed this post because it didn't have the tag 'deseq2'. I'm fixing that now and will answer. ...
written 1 day ago by Michael Love17k
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Answer: A: DESEq2 Principal Component Analysis with different genes biotypes (protein codin
... You should add an indexing step before calling plotPCA: idx <- ... # identify the relevant gene sub-types plotPCA(rld[idx,], ...) ...
written 1 day ago by Michael Love17k
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Comment: C: Allele-specific expression with different gene lenghts
... I'd say take a look at how I went about it in the workflow you posted. Yes, there's a critical difference in adding the sample information and identifying which column is which allele or not. ...
written 1 day ago by Michael Love17k
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Answer: A: DESEQ2 design with multiple conditions
... Because the design is such an important part of the data analysis process, we specifically didn't help this step be automated. The great majority of the DESeq2 posts here are analysts who are thinking about exactly how to model their data, what assumptions to make, which coefficients to include, whe ...
written 1 day ago by Michael Love17k
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Comment: C: use deseq2 in asthma
... If you hit a problem, make sure you've typed everything in exactly correct. You can always copy paste to avoid spelling mistakes, e.g.  > library(GenomicFeatures) Error in library(GenomicFeatures) : there is no package called ‘GenomicFeatures’ then copy the name of the missing package instal ...
written 2 days ago by Michael Love17k

Latest awards to Michael Love

Scholar 10 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 10 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 10 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 10 months ago, asked a question with at least 3 up-votes. For recount counts in the example experiment
Appreciated 10 months ago, created a post with more than 5 votes. For A: DESeq2 Model Design
Scholar 10 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 11 months ago, asked a question with at least 3 up-votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Commentator 11 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 11 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 Model Design
Scholar 11 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 11 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 11 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 11 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 11 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 11 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 11 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 11 months ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Appreciated 11 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 11 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 12 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 12 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 12 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 12 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 12 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Appreciated 13 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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