Moderator: Michael Love

gravatar for Michael Love
Michael Love26k
Reputation:
26,010
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
21 hours ago
Joined:
6 years, 9 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 • 5,327 results • page 2 of 533 • next >
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Comment: C: Cannot find header.json in salmon index directory
... So that first line doesn’t match the code thats in GitHub or Bioconductor, meaning you don’t yet have the fixed version of the code. I wonder what could be going on. Maybe try restarting R? Re: 80 samples, tximeta calls tximport so no it won’t change performance. Make sure you’ve allocated sufficie ...
written 3 days ago by Michael Love26k
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Answer: A: Help with DESeq2 design matrix
... Do you expect the subclone to host effect to be the same or different per cell line? If the latter, use `~line + line:condition` For a line-specific condition effect. Condition should take values either subclone or host. Both should be factors. ...
written 3 days ago by Michael Love26k
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Comment: C: Cannot find header.json in salmon index directory
... Can you type out `makeLinkedTxome` in the console, type return and see what the code says? The first line should be ``` indexJson <- file.path(indexDir, "info.json") ``` So I'm confused by it wouldn't be picking it up. You can also run this line of code to check: ``` file.exists(file.path(i ...
written 3 days ago by Michael Love26k
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Comment: C: Does DESeq2 Data_transformation (vsd or rld) Change Clustering (and PCA_plot) Re
... I’d guess the PCA plot is similar here. The hclust result on the distances is not very stable, so I wouldn’t base too much on that alone. It may be more consistent across transformations if you subset to the 500 or 1000 genes with highest variance. ...
written 3 days ago by Michael Love26k
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Answer: A: Does DESeq2 Data_transformation (vsd or rld) Change Clustering (and PCA_plot) Re
... Yes its expected, for example we show different performance in the 2014 paper across these methods. Are you using blind=FALSE? this is recommended if you have large treatment or batch effects. ...
written 3 days ago by Michael Love26k
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Answer: A: Results counts to Deseq object
... Take a look at the vignette and the workflow (linked from top of vignette). We have a lot of documentation where we work through all the basics including object construction. ...
written 3 days ago by Michael Love26k
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Comment: C: DESeq2: experiment with two genotypes and three conditions
... That’s not it, I said you have to add that to what you had not replace with what you had. Eg `list( c(“A”,”B”), c(“C”,”D”) )` This puts A and B in numerator and C and D in denominator. Take a look at the Examples section of ?results ...
written 4 days ago by Michael Love26k
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Comment: C: DEseq2 design matrix for paired samples with batch effects
... Yes the VST data is library size corrected. The column sum is a notoriously bad estimator for whether there are global shifts. Use a boxplot on log scale data (VST output). ...
written 5 days ago by Michael Love26k
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Comment: C: DEseq2 design matrix for paired samples with batch effects
... Ok I see. This could be fit with a model such as: Y = intercept + period + treatment + subject + error And typically the subject effect is modeled with a random effect, leading to a mixed effects model. One option would be to use DESeq2 to scale and variance stabilize the counts with `vst(dds)` an ...
written 5 days ago by Michael Love26k
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Comment: C: Comparing factor levels in deseq2
... Can you look over this related thread for more background: https://support.bioconductor.org/p/117940/#126943 ...
written 5 days ago by Michael Love26k

Latest awards to Michael Love

Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: Multiple groups and two methods to analyse them with DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Prophet 4 months ago, created a post with more than 20 followers. For New function lfcShrink() in DESeq2
Scholar 4 months ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Scholar 4 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 4 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Popular Question 4 months ago, created a question with more than 1,000 views. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 4 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 4 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 4 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 4 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 4 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Appreciated 4 months ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 10 months ago, created an answer that has been accepted. For A: Using altHypothesis with shrunken LFC values in DESeq2
Scholar 10 months ago, created an answer that has been accepted. For A: Unable to find an inherited method for function 'results' for signature '"DESeqD
Scholar 10 months ago, created an answer that has been accepted. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 10 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2 lfcShrink using only dds and res arguments
Scholar 10 months ago, created an answer that has been accepted. For A: Change lower bound 'optim' function in DESeq2::unmix() to 0.001 to prevent error

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