Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Denali
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Last seen:
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Joined:
8 years, 8 months ago
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I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

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Answer: A: featureCounts taking 4-10 hours per BAM file?
... Somethings you might want to think about: How much RAM do you have?; and Is your external HD to blame? Does it go any faster if you move it to your local HD? (hopefully an SSD :-) ...
written 8 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Can Tximport average transcript length be used for GOSeq?
... Yes it can, and it's arguably a better value to use than what is in the database anyway. ...
written 5 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: Installing an older release of Bioconductor
... This may *technically* work, however the bioconductor ecosystem (v3.4, v3.5, etc) is only tested to work against a very specific version of R. Installing bioc packages using anything but `biocLite()` can land you into a mess. It doesn't mean that you can't try, but you'll be on your own if/when thin ...
written 5 weeks ago by Steve Lianoglou ♦ 12k
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Answer: A: Incredibly high/low foldChange
... A 39e6 fold change seems crazy ... but, of course, if a gene has all zero counts in one group, and some counts in another than the fold change is infinite, right? Whatever the case may be, it does warrant further inquiry. This first thing you should do is try to visualize your data. DESeq2 has a " ...
written 7 weeks ago by Steve Lianoglou ♦ 12k
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Answer: A: voom command broken in limma_3.34.5?
... The Error in round(counts) : non-numeric argument to mathematical function you are getting suggests that your counts object isn't what you think it is. What is the output of class(counts) and class(counts[1])? ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Limma RNA seq analysis_VOOM
... It's not stored anywhere in the sense that you are thinking. These covariates are just accounted for inside the linear model. If you want to explore what your data looks like when these covariates are accounted for, take a look at limma's removeBatchEffects function. ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Answer: A: Does bioconductor now has microarray cross-platform merging and normalization me
... You haven't said what you would want to do the cross-platform merging for, but I think you're going down the wrong rabbit hole. Often times people inquire about merging different platforms so that they can combine different studies that are about "the same thing" and increase their N. If this is wh ...
written 4 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Unbalanced experiment with multiple samples from each patient.
... Great answer, as usual, but I think the OP should pay particular attention to the "assuming they are technical replicates" bit of this answer. It might be useful for the OP to elaborate on how repeated "healthy" or "diseased" measures from the same patient are ending up in these data. For instance, ...
written 4 months ago by Steve Lianoglou ♦ 12k
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Answer: A: How to extract the voom normalized value for each observation?
... I doubt you can combine these into a single number in any meaningful way. You need an algorithm that can take observations and their weights and use them productively together ... ...
written 4 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Tac and Bioconductor giving different results
... You are likely right, you shouldn't be seeing such large differences. Again, no one can help you because we can't debug stories -- you need to provide code. You probably want to RMA normalize your data and use limma for analysis. You hopefully have some intuition of the experiment you are analyzing ...
written 5 months ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Scholar 11 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 24 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 24 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 24 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 24 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.0 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.2 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 2.2 years ago, received more than 100 upvotes.
Scholar 2.2 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.5 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.8 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.9 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 3.1 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Oracle 3.2 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 3.2 years ago, voted more than 100 times.
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
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