Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Genentech
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Last seen:
16 hours ago
Joined:
8 years, 6 months ago
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I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

<prev • 1,373 results • page 2 of 138 • next >
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Answer: A: Add new columns to DESeqResults from text file by matching rownames.
... Call as.data.frame on your DESqResults objects before the merge, ie. out <- merge(as.data.frame(result.ASE_Data), geneMap, ...) merge doesn't match by rownames, though, so you will have to specify the correct value for by, or a by.x and by.y combination of the column names in your result.ASE_D ...
written 4 months ago by Steve Lianoglou12k
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Comment: C: Differential expression of nomalised and log2 transformed data in limma
... Your design matrix is constructed from a factor (vector) that is 100 elements long. The first 50 are "1" and the second "50" are "2", but you said yourself that you have 25 elements per group, so ... why are you doing rep(..., each=50)? Fix it so that you have as many labels as samples ... and, btw ...
written 4 months ago by Steve Lianoglou12k
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Answer: A: DESeq2 Which gene used to normalize?
... Unless you specify a set of control genes to use, every gene which has all-non-zero-observations is used. See the help in ?estimateSizeFactors and ?estimateSizeFactorsForMatrix for more information. ...
written 4 months ago by Steve Lianoglou12k
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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 5 months 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 5 months 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 5 months ago by Steve Lianoglou12k
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Comment: C: Is DESeq2 PCAplot already scaled?
... How did you divine that post?   ...
written 5 months 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 5 months 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 5 months 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 5 months ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Scholar 9 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 22 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 22 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 22 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 22 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 22 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 24 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 2.0 years ago, received more than 100 upvotes.
Scholar 2.1 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: "Wobble" patterns for genome searching using Biostrings
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 2.6 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: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 2.9 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 3.1 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 3.1 years ago, voted more than 100 times.
Teacher 3.2 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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