Moderator: Michael Love

gravatar for Michael Love
Michael Love26k
Reputation:
25,890
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
5 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

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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 5 hours 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 1 day 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 1 day 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 1 day ago by Michael Love26k
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Answer: A: Comparing factors in deseq2
... Take a look at the examples in the ?results man page. There are examples of how to do this. ...
written 1 day ago by Michael Love26k
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Comment: C: how to correct for age using Deseq2
... There's a lot going on here, and it doesn't seem to be a question about how to use the software but about what statistical analysis should be done. That conversation should really be had with a statistician who you can find to collaborate with. I was pointing you the vignette with respect to how y ...
written 1 day ago by Michael Love26k
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Comment: C: DESeq2: 5 Conditions (B vs C) vs (D vs B)
... Be careful about the terms here, and read carefully over the help pages. I said above to put A and D in the numerator. You have put A and **B** in the numerator and C and D in the denominator. See the help page for `?results`: > a list of 2 character vectors: the names of the fold changes for t ...
written 2 days ago by Michael Love26k
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Answer: A: Normalized counts access in DESeq2 R: with and without batch
... No, size factors dont use the design. In order to get data corrected for batch, we recommend VST followed by removal of the batch effect with a linear regression, see the FAQ in the vignette. ...
written 2 days ago by Michael Love26k
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Comment: C: DESeq2: 5 Conditions (B vs C) vs (D vs B)
... Sure, you can do that with the list style on contrast. Just rearrange so that A and D are in the numerator and B and C in the denominator. ...
written 2 days ago by Michael Love26k
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Answer: A: DEseq2 design matrix for paired samples with batch effects
... So you have two samples per patient? Condition 1 treated and condition 2 treated but not control? And then there is the week variable splitting the patients in two. ...
written 2 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 3 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 3 months ago, created a post with more than 20 followers. For New function lfcShrink() in DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
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: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
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
Popular Question 3 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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