Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
11,590
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Trusted
Location:
Genentech
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
7 years, 10 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 • 1,337 results • page 1 of 134 • next >
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Comment: C: Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased da
... Not related to salmon, but why would the (R|F)PKM screw up your differential expression analysis when you used featureCounts? I mean, if you ran featureCounts to get counts over your gene features, the most natural thing I could think of doing would be to then feed those counts directly into edgeR, ...
written 7 days ago by Steve Lianoglou12k
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Comment: C: error installing cummeRbund in R studio (Windows desktop)
... Some comment as before, you are missing a required package "RSQLite". You need to carefully read through the "Error:" messages you are getting and sort those out. It's not clear to me how this happened, but your installation seems quite broken for one reason or another. When you start from a "clean ...
written 9 days ago by Steve Lianoglou12k
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Answer: A: error installing cummeRbund in R studio (Windows desktop)
... It looks like you've somehow ended up with an incomplete installation because somehow somewhere someone is trying to load the matrixStats package, which doesn't appear to be installed. Try installing that first, and try again. install.packages("matrixStats")   ...
written 10 days ago by Steve Lianoglou12k
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Great, glad to hear that and thank you for taking the time to follow up and close the loop on this. ...
written 10 days ago by Steve Lianoglou12k
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Answer: A: WGCNA always requires trait data?
... You don't need (and can't use, AFAIK) trait data for module creation, so if your goal is to just identify modules of co-regulated genes, then your'e good. Often people want to the associate the activation/expression-level of modules to "traits" but that's a downstream step ... ...
written 20 days ago by Steve Lianoglou12k
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Comment: C: Dr. Armin Ahmadvand
... You need to create a numeric matrix from your data.frame. You would do this by calling as.matrix(XXX) where XXX is the subset of columns in your Negin_AE_BD data.frame that have the numeric values you are trying to plot. You would then set rownames()<- of your numeric matrix to be the geneID colu ...
written 21 days ago by Steve Lianoglou12k
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Answer: A: Problem with locfit after update bioconductor to Bioconductor version 3.5
... Just try reinstalling it. Whenever you upgrade R you should reinstall all of your packages ... ...
written 22 days ago by Steve Lianoglou12k
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Comment: C: Is mapId supposed to concatenate multiVals?
... Thank you for taking the time to do that, Johannes! ...
written 27 days ago by Steve Lianoglou12k
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Answer: A: Dr. Armin Ahmadvand
... I would guess your Negin_AD_BD objet isn't what you think it is. It needs to be a numeric matrix, with no missing values. Check the output of the following: class(Negin_AD_BD) (is it matrix?) class(Negin_AD_BD[1]) (is it numeric?) any(is.na(Negin_AD_BD)) (is it FALSE?) Also, you'll probably ...
written 4 weeks ago by Steve Lianoglou12k
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Answer: A: Limma filtering based on treatment group
... No. Don't do that. Your filtering criterion needs to be independent of the test statistic:  http://m.pnas.org/content/107/21/9546.long     ...
written 5 weeks ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Scholar 5 weeks ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 14 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 14 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 14 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 14 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 14 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 15 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 16 months ago, received more than 100 upvotes.
Scholar 16 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: "Wobble" patterns for genome searching using Biostrings
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 23 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.1 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
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
Oracle 2.4 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 2.4 years ago, voted more than 100 times.
Teacher 2.5 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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