Moderator: Michael Love

gravatar for Michael Love
Michael Love11k
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10,570
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Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
19 hours ago
Joined:
3 years, 11 months 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 • 1,947 results • page 1 of 195 • next >
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Comment: C: How to normalize chromatin and RNA-Seq data together ?
... "Even that's a bit sketchy, because differences are inevitable - for example, why would you ever expect a 2-fold increase in chromatin accessibility to result in a 2-fold increase in transcription?" => agree ...
written 19 hours ago by Michael Love11k
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Answer: A: DESeq2: Difference in rlog and vst values if run transform before or after runni
... Not sure why you're not getting equality, at least within tolerance. Can you use all.equal(x,y) instead, so we can see what the mean relative difference is? Here's what I get: > dds <- makeExampleDESeqDataSet() > rld <- rlog(dds, blind=FALSE) > dds <- DESeq(dds) estimating size ...
written 22 hours ago by Michael Love11k
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Comment: C: Using 'tximport' library for downstream DGE after quantifying with Kallisto
... I moved this post from an 'Answer' to a 'Comment' You need to come up with a way to group transcripts into genes if you want to summarize your transcripts into genes. I believe that new software from Alicia Oshlack's group can help with this:  https://github.com/Oshlack/Lace/wiki https://github. ...
written 23 hours ago by Michael Love11k
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Comment: C: Designing a contrast in DESEQ
... Adding patient as a term should help remove the variation across patient, and improve sensitivity. This is potentially why you have more DE genes. Note that you should follow the recommendations in the vignette and always put the variable of interest (group) at the END of the design formula: ~ pati ...
written 23 hours ago by Michael Love11k
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Comment: C: DESeq2 design confusion with three factors
... hi Vince, the contrasts in (a) and (b) are correct. Except for (b) you won't be able to use a formula for the design, you'll have to supply a model matrix in which you remove the columns which are all zeros, there is some example code in the vignette for this. For (c), you don't really have enough ...
written 23 hours ago by Michael Love11k
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Answer: A: Removing Zero Counts from results(dds, contrast=c("condition", "x", "y")) vs rem
... Read the vignette section on "independent filtering". The short answer is that you don't have to remove the extra small counts when you are comparing two groups, because this is performed automatically when you build a results table. See the vignette and ?results for details. ...
written 23 hours ago by Michael Love11k
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Answer: A: How to normalize chromatin and RNA-Seq data together ?
... DESeq2 won't help you correlate nearby chromatin to gene expression. It doesn't offer any built-in functionality for that. The case when people put e.g. RNA-seq and other types of assay (ChIP or ATAC) in the same dds object, is to answer if the fold change due to treatment within one assay is diffe ...
written 23 hours ago by Michael Love11k
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Comment: C: Extract results from DESeq2 object for base level of term of interest using LRT
... These two scenarios describe one and the same null hypothesis. Let's say you have reference level Z (control), and then other levels A,B,C,... If A=Z, B=Z, C=Z, ... this implies that A=B=C... ...
written 2 days ago by Michael Love11k
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Comment: C: Similar to Tukey Post hoc after ANOVA
... Yes, if you want to selectively report the results (i.e. only describe certain of the 6 comparisons with differential gene expression), I'd recommend correcting over all of the p-values together. You can do this by combining the p-values into one long vector, running p.adjust() over these, and then ...
written 2 days ago by Michael Love11k
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Comment: C: DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq
... hi Zach, Regarding re-running DESeq() after filtering or just re-running results(), I don't have a preference one way or the other. Results might change slightly as there is a lot going on when you re-run DESeq(), I just don't have a reason to recommend you one way or the other. Regarding alpha, y ...
written 3 days ago by Michael Love11k

Latest awards to Michael Love

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 3 days ago, created an answer that has been accepted. For A: trouble installing DESeq2
Scholar 6 days ago, created an answer that has been accepted. For A: trouble installing DESeq2
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 17 days ago, created an answer that has been accepted. For A: trouble installing DESeq2
Appreciated 25 days ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 28 days ago, created an answer that has been accepted. For A: trouble installing DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq is better than DESeq2?
Scholar 10 months ago, created an answer that has been accepted. For A: PCA from deseq and r function differ
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2 results(): 'name' argument and ?equivalent? numeric contrast produce diff
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: DESeq2 rlog function takes too long
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2 MA plot of encode data
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2: Question regarding changes between Bioconductor 3.2 and 3.4 or recent ve
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 multifactor and paired sample analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Analyzing microbiome data (many zero-counts) using DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 results(): 'name' argument and ?equivalent? numeric contrast produce diff
Scholar 10 months ago, created an answer that has been accepted. For A: DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2: Question regarding changes between Bioconductor 3.2 and 3.4 or recent ve
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DESeq2 rlog error
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: deseq2 estimating size factors
Scholar 10 months ago, created an answer that has been accepted. For A: DESEQ2: high number of differentially expressed genes with very high fold chang
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: does pca assume no heteroscedasticity?

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