Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Genentech
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I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

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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 6 weeks ago by Steve Lianoglou12k
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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 7 weeks ago by Steve Lianoglou12k
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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 9 weeks ago by Steve Lianoglou12k
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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 9 weeks ago by Steve Lianoglou12k
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Answer: A: How to extract the voom normalized value for each observation?
... I doubt you can combine these into a single number in any meaningful way. You need an algorithm that can take observations and their weights and use them productively together ... ...
written 11 weeks ago by Steve Lianoglou12k
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Comment: C: Tac and Bioconductor giving different results
... You are likely right, you shouldn't be seeing such large differences. Again, no one can help you because we can't debug stories -- you need to provide code. You probably want to RMA normalize your data and use limma for analysis. You hopefully have some intuition of the experiment you are analyzing ...
written 3 months ago by Steve Lianoglou12k
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Answer: A: Tac and Bioconductor giving different results
... This is an impossible question to answer. Although I (and likely most people here) have never used "TAC affymetrix software" (I guess you mean this?), I imagine there are a multitude of ways to perform an analysis there just as there are many ways to perform an analysis using various bioconductor t ...
written 3 months ago by Steve Lianoglou12k
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Answer: A: Best DEG tool for datasets with FPKM counts?
... For analysis, you will want to log2 transform the fpkm values and use the limma-trend pipeline, see here: https://support.bioconductor.org/p/56275/ As for the gene_id column, you're only looking in the land of "funny looking" gene ids. Take a random sampling of the gene_id values, ie. if you have ...
written 3 months ago by Steve Lianoglou12k
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Comment: C: edgeR cpm filter
... Everything is working as it should and, further, your filtering strategy should be blind to the groups each sample belongs to. You can either increase your filtering threshold (ie. keep <- rowSums(cpm(y) > 2) >=5) if you want to remove more (any) genes, or you can switch to filtering based ...
written 4 months ago by Steve Lianoglou12k
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Comment: C: edgeR cpm filter
... The code itself looks like it should work, so when you say "this doesn't work", what do you mean, exactly? Are you getting an error somewhere, or? Also, if you have 6 replicates per group your keep rowSums threshold should technically be >= 6, but this probably won't change much in the downstrea ...
written 4 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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