Moderator: Michael Love

gravatar for Michael Love
Michael Love17k
Reputation:
17,110
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
a minute ago
Joined:
5 years, 2 months ago
Email:
m****************@gmail.com

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

The Love lab maintains the following R/Bioconductor packages:

and the RNA-seq gene-level workflow.

Posts by Michael Love

<prev • 3,486 results • page 2 of 349 • next >
0
votes
1
answers
46
views
1
answers
Comment: C: steps to get up and down regulated genes using DESeq2
... This is answered in our papers and specifically in the vignette, see the Table of Contents. Please take some time to read over our documentation before posting. I want to focus my time on support questions not covered in the publications and documentation. ...
written 1 day ago by Michael Love17k
0
votes
1
answers
46
views
1
answers
Comment: C: steps to get up and down regulated genes using DESeq2
... Please take a look at our workflow: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html ...
written 1 day ago by Michael Love17k
0
votes
1
answers
46
views
1
answers
Answer: A: steps to get up and down regulated genes using DESeq2
... Replicates are required to test for significance of up and down DE. ...
written 1 day ago by Michael Love17k
0
votes
1
answers
62
views
1
answers
Comment: C: Few significance in DESeq2
... Yes this can induce non uniform null. ...
written 3 days ago by Michael Love17k
0
votes
2
answers
3.9k
views
2
answers
Comment: C: Deseq2 rlog or 'regular' normalization?
... hi jivara, We have extensive documentation. Please read that beforehand. There is a vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html And a workflow for beginners: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc ...
written 3 days ago by Michael Love17k
0
votes
2
answers
3.9k
views
2
answers
Comment: C: Deseq2 rlog or 'regular' normalization?
... You may want to read some internet references on PCA (there are loads). Briefly PC2 is the dimension which captures the second most amount of variance in the samples, while being orthogonal (you can think, roughly, "pointing in a totally different direction") to PC1. ...
written 3 days ago by Michael Love17k
0
votes
2
answers
3.9k
views
2
answers
Comment: C: Deseq2 rlog or 'regular' normalization?
... rlog and vst give log2-like transformed counts. This is also covered in the vignette in detail. ...
written 4 days ago by Michael Love17k
0
votes
1
answers
33
views
1
answers
Answer: A: DeSeq2 for comparison of experimental factors on microbial composition
... DESeq2 can be used to compare counts across groups of samples or other complex experimental designs. Take a look at the paper and the software vignette. The input is a count matrix, and an Negative Binomial model is fit per row (OTU in your case), which takes into account a normalizing offset for se ...
written 4 days ago by Michael Love17k
0
votes
1
answers
47
views
1
answers
Comment: C: Create Ensembl transcript to gene IDs table with R ensembldb package for tximpor
... Take a look at the ensembldb vignette. It’s very detailed  ...
written 4 days ago by Michael Love17k
0
votes
1
answers
168
views
1
answers
Comment: C: DESeq2: Poor dispersion fit, even when a local or custom fit is used
... One more note. estimateDispersions() will be fast, you don't need to parallelize. You only need to run estimateSizeFactors() before this, which is also fast. nbinomWaldTest() is still slow, because you have 100s of conditions and 600 samples.You can easily split across multiple cores and recombine ...
written 5 days ago by Michael Love17k

Latest awards to Michael Love

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Confused in the usage of formula in DESeq or DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Analyzing RNA-Seq data without replicates using DESeq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to get DESeq2 sizefactors from data imported using tximport
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 biais when genes are missing from the annotation?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 rlog function takes too long
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: GC/length bias correction in gene expression quantification - Is CQN necessary i
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: identifying the samples on plotPCA
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Student 10 months ago, asked a question with at least 3 up-votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 batch effect with and without interaction model
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 paired multifactor test
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 batch effect modeling and matrix not full rank
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq is better than DESeq2?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2: add annotations (from data frame) to DESeqDataSet
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: tximport with versioned identifiers
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Normalize to additional variable (brain weight) in DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: deseq2 - many differentially expressed genes
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: deseq2 estimating size factors
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 Model Design
Teacher 10 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 10 months ago, created an answer with at least 3 up-votes. For A: Convert Normalized RNA-Seq counts to TPM after Batch Correction

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 287 users visited in the last hour