Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
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Trusted
Location:
Denali
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Google Scholar Page
Last seen:
6 hours ago
Joined:
10 years, 4 months ago
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s*********@gmail.com

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: PureCN version clashes at GitHub and Bioconductor
... Those 3_X versions refer to the version of bioconductor that they were release for. For instance, the current version of bioconductor is 3.10, which you can see from the News section of the [home page](http://bioconductor.org/), or up top on the [Install page](http://bioconductor.org/install/). Wh ...
written 19 days ago by Steve Lianoglou ♦ 12k
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Comment: C: Limma residuals matrix
... These values (-0.07 and -0.06) are already in log space, no? If not, where are you getting these numbers from? Anyway, assuming we're talking about numbers already in log-space, this shakes out to just being T - R ... ...
written 22 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Limma analysis on a subset of data
... This question comes up fairly often, although admittedly not the easiest to search for. The general advice is that unless you have a very good reason not to, you should run the fit and eBayes step on all of the data, and just make sure you specify your contrasts correctly so that you get the statis ...
written 6 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: Trying to download VIPER
... Be careful, though. It seems like viper is on "deprecation watch" since the package is (apparently) not being properly updated/maintained(?) https://support.bioconductor.org/p/123439/ ...
written 7 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: how to a load workflow package
... How did you install the workflow package? Did you use `BiocManager::install("cytofWorkflow")`, or? ...
written 7 weeks ago by Steve Lianoglou ♦ 12k
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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 8 weeks 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 8 weeks 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 8 weeks 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 9 weeks 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 10 weeks ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Popular Question 11 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
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?
Popular Question 12 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
Popular Question 12 months ago, created a question with more than 1,000 views. For error in bioconductor installation
Teacher 13 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 13 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Scholar 16 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 16 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 2.5 years ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 2.5 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 2.5 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 2.5 years ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 2.5 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 2.5 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Scholar 2.6 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 3.6 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Scholar 3.6 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
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