Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Genentech
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7 years, 7 months ago
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I am a Computational Biologist at Genentech working in Cancer Immunology.

In a previous life, I was studying alternative cleavage and polyadenylation in humans.

Posts by Steve Lianoglou

<prev • 1,314 results • page 1 of 132 • next >
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Comment: C: mirDeep2 edgeR analysis
... You should probably post a new question instead of adding to a comment to this question (which is almost 4 years old, now). Before doing that, though, take note of Ryan's answer. You'd do well do try one of the rnaseq analysis toolkits (edgeR or DESeq2) on your miRNA data. I imagine you have a coun ...
written 4 days ago by Steve Lianoglou12k
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Comment: C: Limma voom mechanism
... I'm not sure if your reply landed before or after Aaron's edit, so I'll just provide a little more help. The text file that it sounds like you want to make can be had by saving the result of a final call to "topTable" after the successful analysis of your RNA-seq data. It's the "successful analysi ...
written 11 days ago by Steve Lianoglou12k
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Answer: A: Question about TCGA barcode
... The meaning of the barcodes are explained quite well here.   ...
written 13 days ago by Steve Lianoglou12k
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Answer: A: Drawing a HeatMapList while retaining the original row order of each heat map
... While I'm definitely no authority on the subject, it seems doubtful given how it seems rowAnnotations work in the context of a HeatmapList. If you're working outside of RStudio, you might consider just creating independent graphics devices and plotting your different heatmaps in each one to compare ...
written 28 days ago by Steve Lianoglou12k
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Comment: C: Hunting for Human Infectious Agents in Cancer using data from Genomics England's
... If only I were a grad student again .:-) Sounds like a really cool project: good luck filling it! Out of curiosity, are their any publicly available details around your SEPATH pipeline? My google-fu is turning up donuts, and would be interested to learn more about it. ...
written 29 days ago by Steve Lianoglou12k
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Comment: C: Using Sailfish estimated read-counts for DESeq2 analysis
... You're replying to a very old question, and I think it'll probably best to post a new question with the your specific issue. That having been said, if you want to incorporate the gene length information and such from tools like salmon (and I guess kallisto, although I haven't played with it much), ...
written 5 weeks ago by Steve Lianoglou12k
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Comment: C: Camera gene set interpretation
... What James is saying is that since your design does not have an intercept term (ie. you are using a "cell means" model), you need to test a contrast among the columns of your design matrix by specifying a vector of coefficients which is as long as the number of columns of your design matrix, and not ...
written 5 weeks ago by Steve Lianoglou12k
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Comment: C: Appropriate design matrix set up in limma for 2-factor approches with NA values
... Yes, you should subset your features after you have removed the samples that you drop. To put it another way, the removal of "unexpressed" genes should be performed on the same exact dataset (ie. same samples) that you will be pushing through your differential expression pipeline. ...
written 5 weeks ago by Steve Lianoglou12k
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Comment: C: RNA-seq paired analysis design
... Hi Gordon. In the post you reference, you mentioned there that you plan to re-write the linear modeling code in limma to store more information from each fit to run around this approximation problem. It sounds like that hasn't been done yet? If not, is it still on the radar, or do you think it's som ...
written 8 weeks ago by Steve Lianoglou12k
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Maybe they're log2(expected_counts + 1) @svlachavas: while the max is 20.3, is the min == 0? If this is the case, we should be able to get back the expected counts by 2**vals - 1, yes? I haven't check this package, so not sure, but I recently tried to download some data (TCGA and whatever else) f ...
written 11 weeks ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Scholar 11 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 11 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 11 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 11 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 13 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 13 months ago, received more than 100 upvotes.
Scholar 14 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 17 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 20 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 22 months ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 2.0 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Oracle 2.2 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 2.2 years ago, voted more than 100 times.
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis

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