Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Denali
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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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Answer: A: Normalization and Quality Control for Multiple scRNAseq Data Sets
... There is a great series of articles written by Aaron Lun, Davis McCarthy, and John Marioni that outline various aspects of working with single cell data in the bioconductor-verse, I will link to both the "release" and "development" version of these articles. If I were you I'd focus on the devel stu ...
written 4 days ago by Steve Lianoglou ♦ 12k
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Comment: C: EdgeR vs DESeq2 with/without lfcShrink
... Did someone call?    ...
written 4 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: CQN offset and edgeR
... From your two results, out of the five genes you are showing, I see three genes whose logFC's have changed slightly, and two genes that are completely different in their identity. ...
written 5 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: CQN offset and edgeR
... Sure, why don't you try to scramble the values in your cqn offset matrix and see if those don't look any different. This is untested, but I think should work: y2 <- y y2$offset <- matrix(sample(y$offset), nrow = nrow(y$offset)) # ... redo the edgeR steps and test the same contrast Also, how ...
written 6 weeks ago by Steve Lianoglou ♦ 12k
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Answer: A: CQN offset and edgeR
... You can make your life a bit easier by following the code provided in the cqn vignette a bit more closely. There you'll see that the cqn glm.offset matrix is added to the DGEList directly So, modifying your code a bit and using Gordon's suggest contrast: mycqn <- cqn(countData,lengths=uCovar$Gen ...
written 6 weeks ago by Steve Lianoglou ♦ 12k
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Answer: A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
... Here are some options: Get the data from this paper, where the reprocessed the TCGA RNA-seq data using subread (GEO link). The recount project has a reprocessed version of the TCGA data. Click on the TCGA tab at the top there. The ARCHS4 project provides the "recount"ed TCGA data as and HDF5 fi ...
written 9 weeks ago by Steve Lianoglou ♦ 12k
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Answer: A: Difficulty extending ExpressionSet
... The RccSet class in the NanoStringQCPro package extends ExpressionSet, and I don't really see any wholesale copying of any code in there at all. ...
written 11 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: Identify the normalized count from differential expression
... If I were you, I'd be explicit about the value of the gene.length parameter in my call to rpkm, but other than that, you can rest assured that it is doing the right thing. If you really want to know what these functions are doing in more detail so that you can compare them with what you are doing m ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Comment: C: PROBLEM WHILE IMPORTING FOR edgeR
... You need to better explain your problem so that people can have some hope of being able to help you. You have left too much to the imagination about the problems you are facing such that it is impossible for anyone to offer any productive help. What is the dataset you are trying to import from? Is ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Answer: A: Bioconductor 3.7 is released
... Congratulations and thank you for all of the hard work everyone puts into this. Just wanted to point out that the workflow links under the  "New Workflows" Section of the release page you pointed to in this post are broken. For example the "simpleSingleCell" workflow points to https://bioconductor. ...
written 5 months ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Scholar 9 weeks ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 9 weeks 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 15 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 15 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 15 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-
Teacher 15 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 15 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 17 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
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: unable to find Lumi package in R
Scholar 2.5 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Scholar 2.5 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.6 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 2.7 years ago, received more than 100 upvotes.
Scholar 2.7 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
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