Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
11,480
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Location:
Genentech
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Google Scholar Page
Last seen:
23 minutes ago
Joined:
7 years, 5 months ago
Email:
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 • 1,305 results • page 1 of 131 • next >
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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 7 days ago by Steve Lianoglou11k
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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 10 days ago by Steve Lianoglou11k
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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 28 days ago by Steve Lianoglou11k
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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 28 days ago by Steve Lianoglou11k
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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 4 weeks ago by Steve Lianoglou11k
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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 6 weeks ago by Steve Lianoglou11k
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Answer: A: DEG analysis of chemo-sensitive vs resistance by limma
... Since you've setup your design with an intercept, the intercept becomes the first level of your "chemosensitivity" factor, which is "Rx Insensitive". The second coefficient tests the log fold change of "Rx Sensitive" over the intercept, so your reported logFC's correspond to "Rx Sensitive - Rx Inse ...
written 6 weeks ago by Steve Lianoglou11k
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Comment: C: DEG analysis of chemo-sensitive vs resistance by limma
... It all depends on how you setup your model, which (as Aaron has pointed out) you have not shown us. Also, it always helps to plot your data. So, you have identified the gene of interest, now you can plot its expression across your groups (sensitive vs resistance) -- the direction of the fold change ...
written 6 weeks ago by Steve Lianoglou11k
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Comment: C: LogFC in Limma
... While you're addressing Ryan's comment, also note that it looks like you are sending raw microarray data into limma. You are going to want to normalize this data first. Minimally, you should take note that limma expects that the expression values be in log2 space. ...
written 6 weeks ago by Steve Lianoglou11k
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Answer: A: M3D package in Bioconductor 3.4
... The rtracklayer package provides rather versatile methods to import a large number of file types used in genomics, bed files certainly being one of them. If all you need is to import BED files, than try the import (or direct call to import.bed) function it provides to do that. ...
written 6 weeks ago by Steve Lianoglou11k

Latest awards to Steve Lianoglou

Scholar 9 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 9 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
Guru 11 months ago, received more than 100 upvotes.
Scholar 11 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 15 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 18 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 20 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 22 months ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
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Teacher 2.1 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 2.2 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
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Scholar 2.3 years ago, created an answer that has been accepted. 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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