Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
12,370
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Trusted
Location:
Denali
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Google Scholar Page
Last seen:
19 hours ago
Joined:
10 years, 2 months ago
Email:
s*********@gmail.com

I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

<prev • 1,444 results • page 1 of 145 • next >
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Comment: C: How to decided on genes linked by differential binding peaks in opposite conditi
... You will have to better formulate the question you are trying to answer with this data before you can get help on deciding what to do after you have collected it. Once the question you have in mind is more clear, likely the things you should do will become more self evident. ...
written 1 day ago by Steve Lianoglou ♦ 12k
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Comment: C: DEseq2 loading library problem
... This seems like a weird one, and not quite sure where to begin. Something seems hosed with your installation. Does this happen when you start a fresh R sesion? If so, something weird might be getting loaded (from an `.RData`) on startup. Perhaps a useful place to start would be to update your post ...
written 1 day ago by Steve Lianoglou ♦ 12k
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Comment: C: Help with the output from mnnCorrect
... Do all of the values in `chosen.hvgs` appear in both `rownames(sce1)` and `rownames(sce2)`? Which is to say, the output of this operation should be empty: ``` setdiff(chosen.hvgs, intersect(rownames(sce1), rownames(sce2))) ``` is it? ...
written 4 days ago by Steve Lianoglou ♦ 12k
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Comment: C: Log2FC data type error in EnhansedVolcano package
... Just FYI: you should add the package name as a tag so that the package maintainer is notified when you post a question about their package. ...
written 10 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... I've got a few points / comments. The first one I think will address the problem you are asking about directly. The biggest error here is that you have defined a contrast matrix, but you aren't using it. I'll take bits and pieces from your code, hopefully it makes sense. ```r cont.matrix <- mak ...
written 16 days ago by Steve Lianoglou ♦ 12k
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Comment: C: DESeq2 very high log2foldchange values
... > What can be a potential reason for that? looking at the raw counts for these genes clearly shows they present only in the treatment group (average of 4500 vs. 0 in the control). It would seem that you just answered your own question, no? In your opinion, what would would be a better estimate ...
written 27 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Subsetting a data frame generated by topTable() {limma}
... Let’s assume `ttr` is the result from `topTable`, you can do: ``` ttr.sub <- subset(ttr, adj.P.Val < 0.05 & abs(logFC) > 0.5) ``` As an aside, consider looking at the limma::treat() if you want to test against a logFC threshold. ...
written 4 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: SGSeq: core dumped after running convertToSGFeatures() method
... Perhaps it would be helpful where in the codebase this is triggered? You might be able to get that info by calling traceback() right after the error is thrown, which hopefully will bring up the function call stack. Also compare the R and package versions from running sessionInfo() on the failing s ...
written 6 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: SGSeq: core dumped after running convertToSGFeatures() method
... Does this happen every time? I think it's for anyone to tell who is at fault ... seems something more fundamental than SGSeq, though. Have you tried running this on a different (third) computer? Your personal one, perhaps, or perhaps a linux machine you provision from AWS or something? You've got ...
written 6 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: Limma residuals matrix
... Well, I'll be. It does look like there is a `limma::residuals.MArrayLM` function defined. Try `residuals(fit, eset)` and see how it compares to `resids` above ... ...
written 9 weeks ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Popular Question 9 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Popular Question 10 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
Popular Question 10 months ago, created a question with more than 1,000 views. For error in bioconductor installation
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Scholar 11 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Scholar 14 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. 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 C: DEseq2 with limited gene set
Scholar 2.3 years ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: when to apply quantile normalization with voom in limma/voom framework with RNA-
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Scholar 2.4 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 3.5 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Scholar 3.5 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
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