User: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth1.6k
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Australia
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http://www.statsci.org...
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Last seen:
4 hours ago
Joined:
5 years, 8 months ago
Email:
s****@wehi.edu.au

Joint Head of the Bioinformatics Division at the Walter and Eliza Hall Institute of Medical Research.

My research group created the limma, edgeR, goseq, Rsubread, csaw and diffHic packages, all part of the Bioconductor project.

Posts by Gordon Smyth

<prev • 110 results • page 1 of 11 • next >
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Comment: C: The results (logFC) are not consistence (edgeR packages)
... I'm not convinced that there is any problem. How have you judged that the genes SHOULD have the same logFC? None of the code you show in your question would allow you to make that judgement. What "original data" have you looked at and how? ...
written 10 days ago by Gordon Smyth1.6k
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Comment: C: The results (logFC) are not consistence (edgeR packages)
... No, that's not what I mean. If you unlog logCPM you will just get CPM, not logFC. I don't understand why you're not simply using `topTags(model)` which shows you the differentially expressed genes and their logFCs. I don't follow what else you are trying to do or what problem you see. Your code `` ...
written 10 days ago by Gordon Smyth1.6k
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Answer: A: The results (logFC) are not consistence (edgeR packages)
... edgeR logFCs are always consistent with the counts and the data, so the title of your question can't be correct. You can't judge expression changes just by looking at the matrix of counts, because the different library sizes for each sample need to be taken into account as well. To examine the data ...
written 10 days ago by Gordon Smyth1.6k
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Comment: C: The results (logFC) are not consistence (edgeR packages)
... They are in the same order. ...
written 10 days ago by Gordon Smyth1.6k
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Answer: A: Why 'filterByExpr' does not eliminate low read counts from the expression data?
... The filtering appears to have worked correctly. The genes you show have highy significant expression differences between groups, so they are not the sort of genes that one would want to remove from the analysis. The purpose of filtering is to remove genes that have too few reads to establish any wo ...
written 10 days ago by Gordon Smyth1.6k
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Comment: C: Trying to understand the maths behind one Limma function
... No problem, trying to understand the math is good. I was a worried earlier that you might get distracted by focusing on code steps you didn't understand to the detriment of understanding the concept and the math (because I see that happen often). But the answers have included concepts so it's a good ...
written 29 days ago by Gordon Smyth1.6k
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Comment: C: DEG analysis between 2 samples using edger
... This question has been answered a number of times, for example: https://www.biostars.org/p/266211/ ...
written 4 weeks ago by Gordon Smyth1.6k
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Answer: A: DEG analysis between 2 samples using edger
... > Now I am dealing with the case that my sample1 has 2 biological replicates and sample2 is only one replicate. You have at least some biological replication so you can use edgeR. You do not need replication in every group. > I want to compare these 2 samples to do DEG analysis. I went over ...
written 4 weeks ago by Gordon Smyth1.6k
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Comment: C: GO enrichment analysis graphs after goseq: any easy solutions?
... Cross-posted https://support.bioconductor.org/p/124909/ ...
written 6 weeks ago by Gordon Smyth1.6k
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Answer: A: How to get read counts on transcript level using featurecounts?
... I am one of the featureCounts authors. Do you want do conduct analyses for genes, or do you need individual results for all the isoform variations of each gene? The "isoforms" tend to be called "transcripts" in the RNA-seq literature. The featureCounts help page you link to is designed to generate ...
written 3 months ago by Gordon Smyth1.6k

Latest awards to Gordon Smyth

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 9 days ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Supporter 12 days ago, voted at least 25 times.
Commentator 27 days ago, created a comment with at least 3 up-votes. For C: Trying to understand the maths behind one Limma function
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Differential expression: replicates in one condition, no replicates in the other
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Centurion 3 months ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 5 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 6 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Guru 7 months ago, received more than 100 upvotes.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 7 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 11 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 14 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 14 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 14 months ago, created an answer that has been accepted. For A: Differential expression: replicates in one condition, no replicates in the other

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