Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
Reputation:
11,730
Status:
Trusted
Location:
Genentech
Scholar ID:
Google Scholar Page
Last seen:
1 day, 2 hours ago
Joined:
8 years, 1 month 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 • 1,360 results • page 1 of 136 • next >
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Answer: A: Expression profile from $E from Voom
... 1) expression profile in Elist has performed log(CPM) and been normalized for library size, right? Yes 2) Has the expression profile in Elist incorporated the precision weights (represented as $weights in v object) yet? No Note that if you want to use the expression data in your voomed "v" objec ...
written 1 day ago by Steve Lianoglou12k
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Answer: A: Treat Method - number of DE genes
... I'm not really sure what the issue is that you are trying to chase down is. I would recommend, however, that you don't keep updating your question and changing it slightly after interacting with Gordon, but maybe ask a different question that is specific to the new problem you think you are facing. ...
written 3 days ago by Steve Lianoglou12k
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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 15 days ago by Steve Lianoglou12k
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Comment: C: Is DESeq2 PCAplot already scaled?
... How did you divine that post?   ...
written 15 days 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 16 days 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 17 days 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 18 days 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 21 days 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 23 days ago by Steve Lianoglou12k
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Comment: C: Can I ask questions on packages from CRAN?
... ... or stackoverflow, too.   ...
written 4 weeks ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Scholar 4 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 17 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 17 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 17 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 17 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 17 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 17 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
Guru 19 months ago, received more than 100 upvotes.
Scholar 19 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 23 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
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: Perform limma on a subset of genes of interest
Scholar 2.2 years ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.4 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 2.5 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Oracle 2.6 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 2.7 years ago, voted more than 100 times.
Teacher 2.8 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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