Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Denali
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Last seen:
7 hours ago
Joined:
9 years, 10 months ago
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I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

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Comment: C: How to determine the cause of no difference between treatments in rnaseq?
... No, unfortunately it wouldn't make sense to encode the design in this way as there's no replication within your `ind` factor. ...
written 16 hours ago by Steve Lianoglou ♦ 12k
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Comment: C: How to determine the cause of no difference between treatments in rnaseq?
... Note that an FDR of .01 is *quite* conservative, going with an FDR <= 0.10 is not uncommon so take a look at that. As Aaron points out though, there are many reasons for not detecting any DE genes. Maybe the effect of the treatment isnt vere big at all, in which case more replicates will (always ...
written 11 days ago by Steve Lianoglou ♦ 12k
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Comment: C: Too many DEGs
... Can you edit this post and show the code you used for the analysis? ...
written 11 days ago by Steve Lianoglou ♦ 12k
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Answer: A: DESeq2 GLM modelling and Wald's test
... I'm not entirely clear on what you are asking, but I'll take a stab at covering some of the things I think you are inquiring about. **Why can't I just use a "normal" wald or t-test on my data? Why do I have to use some special machinery (like DESeq2)?** There have been a number of methods develope ...
written 11 days ago by Steve Lianoglou ♦ 12k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... perfect, thanks for the tips! :-) ...
written 12 days ago by Steve Lianoglou ♦ 12k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... ![recursion][1] [1]: https://i.imgur.com/mXMKZiq.png ...
written 12 days ago by Steve Lianoglou ♦ 12k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... Can you add more details (code) to your question, please? 1. Can you share a bit of your `$samples` data.frame and show us the code you used to generate the design and the fit? 2. Where did you get these fitted values from? Is it off of some `$fitted.values` somewhere? ...
written 12 days ago by Steve Lianoglou ♦ 12k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... I updated this post -- was the first time I used imgur, actually, so wasn't sure what URL hacking was necessary to get the image to show up. You don't copy & paste the URL of the image page from imgur (which is `https://imgur.com/a/oxlZBoo`), but rather you have to right click on the image itse ...
written 12 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Using already normalized counts
... The most preferable choice is to go back to the person who sent you the Excel sheet and ask them if you can get the raw counts, instead. If you can't do that, I think your best bet is to log transform the normalized counts (if they aren't already) and use the "limma-trend" pipeline, which is "stand ...
written 20 days ago by Steve Lianoglou ♦ 12k
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Answer: A: Bioconductor support site search missing results?
... This isn't really answering the question, but rather suggesting an alternative which has been suggested to others previously for you to try which should get you more relevant results:: just use google. Punch in whatever search terms you want into google, and append `site:support.bioconductor.org` a ...
written 5 weeks ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Popular Question 6 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
Popular Question 6 months ago, created a question with more than 1,000 views. For error in bioconductor installation
Scholar 7 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 7 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 10 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 10 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 24 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 24 months 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 24 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 24 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 24 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 24 months 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-
Scholar 2.1 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Scholar 3.2 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Scholar 3.2 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 3.2 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 3.2 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
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