Moderator: Steve Lianoglou

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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: 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 7 days 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 22 days 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 6 weeks 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 6 weeks 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 3 months ago by Steve Lianoglou ♦ 12k
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Answer: A: PCA analysis in R for 780 genes in 20 samples.
... It looks like you might benefit from some general introductory materials to PCA, and for that you might try reading through some of the materials made available on the factominer website: http://factominer.free.fr/   ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Answer: A: featureCounts taking 4-10 hours per BAM file?
... Somethings you might want to think about: How much RAM do you have?; and Is your external HD to blame? Does it go any faster if you move it to your local HD? (hopefully an SSD :-) ...
written 4 months ago by Steve Lianoglou ♦ 12k
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Answer: A: Can Tximport average transcript length be used for GOSeq?
... Yes it can, and it's arguably a better value to use than what is in the database anyway. ...
written 5 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Installing an older release of Bioconductor
... This may *technically* work, however the bioconductor ecosystem (v3.4, v3.5, etc) is only tested to work against a very specific version of R. Installing bioc packages using anything but `biocLite()` can land you into a mess. It doesn't mean that you can't try, but you'll be on your own if/when thin ...
written 5 months ago by Steve Lianoglou ♦ 12k
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Answer: A: Incredibly high/low foldChange
... A 39e6 fold change seems crazy ... but, of course, if a gene has all zero counts in one group, and some counts in another than the fold change is infinite, right? Whatever the case may be, it does warrant further inquiry. This first thing you should do is try to visualize your data. DESeq2 has a " ...
written 5 months ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Good Answer 13 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 13 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 13 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 13 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Scholar 13 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 C: DEseq2 with limited gene set
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
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: unable to find Lumi package in R
Scholar 2.3 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Scholar 2.3 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 2.4 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 A: unable to find Lumi package in R
Guru 2.5 years ago, received more than 100 upvotes.
Scholar 2.5 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.8 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
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