Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Genentech
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7 years, 6 months ago
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s*********@gmail.com

I am a Computational Biologist at Genentech working in Cancer Immunology.

In a previous life, I was studying alternative cleavage and polyadenylation in humans.

Posts by Steve Lianoglou

<prev • 1,309 results • page 1 of 131 • next >
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Comment: C: Using Sailfish estimated read-counts for DESeq2 analysis
... You're replying to a very old question, and I think it'll probably best to post a new question with the your specific issue. That having been said, if you want to incorporate the gene length information and such from tools like salmon (and I guess kallisto, although I haven't played with it much), ...
written 2 days ago by Steve Lianoglou12k
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Comment: C: Camera gene set interpretation
... What James is saying is that since your design does not have an intercept term (ie. you are using a "cell means" model), you need to test a contrast among the columns of your design matrix by specifying a vector of coefficients which is as long as the number of columns of your design matrix, and not ...
written 4 days ago by Steve Lianoglou12k
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Comment: C: Appropriate design matrix set up in limma for 2-factor approches with NA values
... Yes, you should subset your features after you have removed the samples that you drop. To put it another way, the removal of "unexpressed" genes should be performed on the same exact dataset (ie. same samples) that you will be pushing through your differential expression pipeline. ...
written 5 days ago by Steve Lianoglou12k
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Comment: C: RNA-seq paired analysis design
... Hi Gordon. In the post you reference, you mentioned there that you plan to re-write the linear modeling code in limma to store more information from each fit to run around this approximation problem. It sounds like that hasn't been done yet? If not, is it still on the radar, or do you think it's som ...
written 22 days ago by Steve Lianoglou12k
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Maybe they're log2(expected_counts + 1) @svlachavas: while the max is 20.3, is the min == 0? If this is the case, we should be able to get back the expected counts by 2**vals - 1, yes? I haven't check this package, so not sure, but I recently tried to download some data (TCGA and whatever else) f ...
written 6 weeks ago by Steve Lianoglou12k
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Answer: A: Creating design matrix in LIMMA
... Woops -- provided a boneheaded answer in haste. Had a momentary lapse of reason regarding the nuts and bolts of two-color arrays. The details of my original answer have been redacted to mitigate any damage this might cause a wary future traveler ... Thanks to Ryan for the correction   ...
written 6 weeks ago by Steve Lianoglou12k
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Comment: C: Why does rlog and vst use normalized counts?
... Noting the fact that you are explicitly talking about single cell RNA-seq data is probably something worth updating your question to point out :-) Unfortunately I haven't had the opportunity to really dig into the universe of single cell rnaseq. The first concern I'd have with using DESeq2's rlog o ...
written 9 weeks ago by Steve Lianoglou12k
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Answer: A: Why does rlog and vst use normalized counts?
... Presumably you want your exploratory plots to reveal something about the underlying biology of your experiment. In this case you absolutely want to used some form of normalized counts, and (likely almost) never the raw data itself. To a first approximation, using the normalized counts side steps th ...
written 9 weeks ago by Steve Lianoglou12k
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Comment: C: design of edgeR GLM test
... Creating the right design and contrast can be tricky with multiple factors interacting with each other. Read through the edgeR and limma user guides and look for the sections that explain how to reparameterize these as a one-way layout (for instance, section 4.4.6 of this edgeRUsersGuide). Construc ...
written 9 weeks ago by Steve Lianoglou12k
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Comment: C: DEG analysis of chemo-sensitive vs resistance by limma
... the negative log fold change means that the gene is expressed higher in the insensitive samples. ...
written 11 weeks ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Scholar 10 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 10 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 10 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 10 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 11 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 12 months ago, received more than 100 upvotes.
Scholar 12 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 16 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 19 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 21 months ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 23 months ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Oracle 2.1 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 2.1 years ago, voted more than 100 times.
Teacher 2.2 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
Teacher 2.3 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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