Moderator: Michael Love

gravatar for Michael Love
Michael Love24k
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23,530
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Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
9 hours ago
Joined:
6 years, 3 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:

the RNA-seq gene-level workflow, and the RNA-seq DTU workflow.

Posts by Michael Love

<prev • 4,831 results • page 1 of 484 • next >
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Answer: A: Error in function classes fdef mtable unable to find an inherited method for fun
... You need to provide all of your code and error messages copied from console or else it’s very difficult for anyone to provide help. See the posting guide. ...
written 9 hours ago by Michael Love24k
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Comment: C: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
... I might try SVA or RUV. Another thing I would do is find a batch-y gene (via an LRT removing the batch variable) and look at plotCounts() for these genes to see if the batch effect is consistent. The important thing for DE analysis is what happens at the gene level, while the PCA is just a QC plot ...
written 11 hours ago by Michael Love24k
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Answer: A: DESeqDataSetFromTximport gives <Object with null pointer>
... I can't read your code at all. Where do you create the results object? I didn't see any code using the `results` function. What's the issue exactly? ...
written 11 hours ago by Michael Love24k
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Answer: A: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
... What has happened when you run the `removeBatchEffect` function is to remove shifts in the group means associated with the grouping factor you provide, per row of the matrix. It seems like the shift is not shared across the conditions. Are these really just two batches, or where the condition sample ...
written 11 hours ago by Michael Love24k
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Answer: A: [DESeq2] sequin [ANAQUIN] correction, too many factors in model
... Going in depth into how to normalize here is beyond the software support I can provide at the moment. If you have spike ins, you can use these to normalize with `controlGenes` described in `?estimateSizeFactors`. And I like to use MultiQC and PCA plots (see vignette and workflow) to examine batch ef ...
written 14 hours ago by Michael Love24k
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Comment: C: tximport discrepancy between TPMs and lengthScaledTPMs
... I think if this sample is peculiar among your other samples as having 67% of the TPM from one gene, then the counts from abundance approach may not work. But you may also need to discard that samples for QC reasons? ...
written 18 hours ago by Michael Love24k
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Comment: C: [DeSeq2] Developmental timeline across seasons with non-independent sampling
... So you can use a design of `~individual + season + stage + season:stage`. Q: *"But I wonder if this will remove the within season differences between stages, which I am interested in as well"* This design gives you season-specific differences across stage. Each season has it's own set of differenc ...
written 19 hours ago by Michael Love24k
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Answer: A: [DeSeq2] Developmental timeline across seasons with non-independent sampling
... Is individual 1 from Fall the same individual as 1 from Spring? ...
written 20 hours ago by Michael Love24k
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Answer: A: Importing Salmon counts with tximport with host and virus genomes
... Let me just explain what `tximport` does for gene summarization: for every transcript in the `quant.sf` file, it looks up the gene name, and then collapses the information from the transcript level to the gene level. If you want the viral transcripts to pass through without being summarized, you sho ...
written 20 hours ago by Michael Love24k
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Comment: C: Any way to add a gene-level annotation to my Affymetrix expression data in R?
... This post has nothing to do with DESeq2 so I am removing the tag ...
written 23 hours ago by Michael Love24k

Latest awards to Michael Love

Scholar 5 months ago, created an answer that has been accepted. For A: DESeq2 why estimate dispersion on log scale
Scholar 5 months ago, created an answer that has been accepted. For A: Unexpected differences in results from paired analysis with DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: Add new columns to DESeqResults from text file by matching rownames.
Scholar 5 months ago, created an answer that has been accepted. For A: DESeq2 comparing differential expression results
Scholar 5 months ago, created an answer that has been accepted. For A: DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
Scholar 5 months ago, created an answer that has been accepted. For A: Age covariate continuous vs. categorical
Scholar 5 months ago, created an answer that has been accepted. For A: Altering design following DESeqDataSetFromMatrix and DESeq
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Scholar 5 months ago, created an answer that has been accepted. For A: calculate foldchange after rlogTransformation
Scholar 5 months ago, created an answer that has been accepted. For A: tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: DESeq2 baseMean values for each sample
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: [DESeq2] time series strain-specific differences over time
Scholar 5 months ago, created an answer that has been accepted. For A: DESEQ2 design with multiple conditions
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: clarification of time-series analysis
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Normalization using DESeq
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: [DESEQ2] How to access the normalized data of a DESeqDataSet
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
Commentator 5 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?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale
Scholar 5 months ago, created an answer that has been accepted. For A: Get the countsFromAbundance as limma input
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What doest this p.value distribution mean?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Common differentially expressed genes between two cell lines
Scholar 5 months ago, created an answer that has been accepted. For A: Common differentially expressed genes between two cell lines
Scholar 5 months ago, created an answer that has been accepted. For A: Get release date for version of DESeq2

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