Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
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Genentech
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4 hours ago
Joined:
8 years, 3 months ago
Email:
s*********@gmail.com

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 • 1,368 results • page 2 of 137 • next >
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Comment: C: Is DESeq2 PCAplot already scaled?
... nice move -- strangely(?), it's also the it's also the first on the second page for me, too. Maybe the search box on this site should just urlencode a google query with site:support.bioconductor.org appended to the end and bypass the internal search functionality entirely. ...
written 11 weeks ago by Steve Lianoglou12k
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Comment: C: Is DESeq2 PCAplot already scaled?
... How did you divine that post?   ...
written 11 weeks ago by Steve Lianoglou12k
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Comment: C: Is DESeq2 PCAplot already scaled?
... I've tried to find that post several times now, too! Sadly I've had no luck with it either :-/ ...
written 11 weeks ago by Steve Lianoglou12k
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Answer: A: Is DESeq2 PCAplot already scaled?
... You can take a look at the source for plotPCA by fetching it like so: library(DESeq2) getMethod("plotPCA", "DESeqTransform") You will find in there the call to prcomp that does the PCA, namely: pca <- prcomp(t(assay(object)[select, ])) and a call to ?prcomp will show you the default values for ...
written 11 weeks ago by Steve Lianoglou12k
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Comment: C: error with rbind fill in Mac
... Ok, but you still need to show us the code you are running that throws this error ...
written 11 weeks ago by Steve Lianoglou12k
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Comment: C: error with rbind fill in Mac
... There's so little information to go on for us here, that no one really has any hope of trying to help you. Can you please provide the code you used that throws the error? You say that the error even happens with "the example data they provided" so producing a fully reproducible example should be ea ...
written 11 weeks ago by Steve Lianoglou12k
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Answer: A: DEseq package statistical test
... Take a look at the ?DESeq2 help file and take note of the function signature: DESeq(object, test = c("Wald", "LRT"), fitType = c("parametric", "local", "mean"), betaPrior, full = design(object), reduced, quiet = FALSE, minReplicatesForReplace = 7, modelMatrixType, parallel = FALSE, BPPARAM = ...
written 12 weeks ago by Steve Lianoglou12k
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Comment: C: Can I ask questions on packages from CRAN?
... ... or stackoverflow, too.   ...
written 3 months ago by Steve Lianoglou12k
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Keep in mind that this is more of an art than a science. With that having been said, in in your case of 286 samples in one or 80 in another, if I were to use the same "filtering idiom" (expressed over X cpm in Y samples) I personally wouldn't go up to 80. In my mind, these sample subsets are big en ...
written 3 months ago by Steve Lianoglou12k
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Simply because there are 14 samples in the smallest "experimental group" (in this case "adjacentnormal"). Given that, I reckon you can divine the answers to your "why not more or less" questions by playing out a few thought experiments in your mind but to answer one specifically: if you required mo ...
written 3 months ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Scholar 6 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 19 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 19 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 19 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 19 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 19 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 21 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 21 months ago, received more than 100 upvotes.
Scholar 22 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.1 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
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
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 2.4 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.5 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 2.7 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 2.8 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 2.8 years ago, voted more than 100 times.
Teacher 3.0 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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