Moderator: Steve Lianoglou

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I am currently a Computational Biologist at Denali.

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Posts by Steve Lianoglou

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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 7 weeks 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 8 weeks 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 9 weeks 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 3 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 3 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 3 months ago by Steve Lianoglou ♦ 12k
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Answer: A: voom command broken in limma_3.34.5?
... The Error in round(counts) : non-numeric argument to mathematical function you are getting suggests that your counts object isn't what you think it is. What is the output of class(counts) and class(counts[1])? ...
written 5 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Limma RNA seq analysis_VOOM
... It's not stored anywhere in the sense that you are thinking. These covariates are just accounted for inside the linear model. If you want to explore what your data looks like when these covariates are accounted for, take a look at limma's removeBatchEffects function. ...
written 5 months ago by Steve Lianoglou ♦ 12k
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Answer: A: Does bioconductor now has microarray cross-platform merging and normalization me
... You haven't said what you would want to do the cross-platform merging for, but I think you're going down the wrong rabbit hole. Often times people inquire about merging different platforms so that they can combine different studies that are about "the same thing" and increase their N. If this is wh ...
written 6 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Unbalanced experiment with multiple samples from each patient.
... Great answer, as usual, but I think the OP should pay particular attention to the "assuming they are technical replicates" bit of this answer. It might be useful for the OP to elaborate on how repeated "healthy" or "diseased" measures from the same patient are ending up in these data. For instance, ...
written 6 months ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Good Answer 12 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 12 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 12 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 12 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Scholar 12 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 13 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Scholar 2.2 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 2.2 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 2.2 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Scholar 2.2 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.3 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 2.4 years ago, received more than 100 upvotes.
Scholar 2.4 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.7 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 2.9 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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