Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth38k
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Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
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Google Scholar Page
Last seen:
3 hours ago
Joined:
16 years, 6 months ago
Email:
s****@wehi.edu.au

Joint Head of 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.

Posts by Gordon Smyth

<prev • 3,711 results • page 2 of 372 • next >
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Answer: A: the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
... All the quantities supplied by edgeR are well documented, just read the help pages or User's Guide or worked case studies. edgeR avoids ambiguous terms like "normalized count" in favour of explicit functions such as `cpm` and `rpkm`. The edgeR User's Guide has a Section called *Clustering, heatmaps ...
written 7 days ago by Gordon Smyth38k
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Comment: C: design matrix for 4 groups in edgeR
... But you haven't defined a contrast. To do a meaningful test of differential expression, you have to compare one group with another. So far, you haven't made any comparison. Which of the other groups do you want to compare infected+treated with? Please have a look at the section of the User's Guide ...
written 10 days ago by Gordon Smyth38k
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Answer: A: Question: design matrix for 4 groups in edgeR
... Why don't you follow the simpler approach that we almost always recommend, which is to combine treatment and infection into one factor with four levels? It's much easier to work with, see Section 3.3.1 of the edgeR User's Guide. ...
written 11 days ago by Gordon Smyth38k
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Comment: C: edgeR DGEList and design matrix
... Your design matrix is correct as it is. For the filtering, you should use ``` fillterByExpr(x, group=treat) ``` or ``` filterByExpr(y, group=treat) ``` ...
written 12 days ago by Gordon Smyth38k
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Comment: C: lmFit very slow if there are missing values
... If there are no weights or NAs then the same QR decomposition can be applied to all genes. Even with NAs, `lmFit` should still be about 20 times faster than looping through the rows with `lm()` and `summary()`. ...
written 13 days ago by Gordon Smyth38k
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Answer: A: edgeR DGEList and design matrix
... To use edgeR pipelines, you need to first filter out non-expressed or very low expressed genes using `filterByExpr()`. See the User's Guide or one of the examples: https://bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html The error you report does not ...
written 13 days ago by Gordon Smyth38k
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Comment: C: Most (90%) DE genes of a contrast were upregulated: implication on the assumptio
... Most normalization methods will have some trouble, not be perfect, when there is a lot of asymmetric DE. But when I say "a lot", I mean as a percentage of the total number of genes, not as a proportion of the DE genes. Your experiment has very little asymmetry. If you have 180 up genes and 20 down g ...
written 14 days ago by Gordon Smyth38k
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Answer: A: Most (90%) DE genes of a contrast were upregulated: implication on the assumptio
... No, TMM does not make any assumption that there are equal numbers of up and down genes The edgeR User's Guide says: > TMM is recommended for most RNA-Seq data where the majority (more than half) of the genes are believed not differentially expressed between any pair of the samples. It doesn't s ...
written 15 days ago by Gordon Smyth38k
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Comment: C: EdgeR mistake- dispersion
... No, that isn't the design matrix. I'm going to make the same suggestion that Mike Love gave you, which is that you would be well advised to consult a bioinformatician or statistician at your own university or institution for help. ...
written 15 days ago by Gordon Smyth38k
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Answer: A: lmFit very slow if there are missing values
... The timings you give show that lmFit is actually very fast, especially so when there are no NAs. You are the first person ever to view that as a "bug". lmFit does an intial scan for NAs or weights and, if they are absent, then it runs a special super-fast algorithm that only works when there are no ...
written 15 days ago by Gordon Smyth38k

Latest awards to Gordon Smyth

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 7 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 12 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 25 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 28 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 29 days ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 4 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Popular Question 7 months ago, created a question with more than 1,000 views. For non-integer counts for edgeR
Scholar 7 months ago, created an answer that has been accepted. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Popular Question 7 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Popular Question 7 months ago, created a question with more than 1,000 views. For Columns used by read.maimages for Agilent arrays
Scholar 7 months ago, created an answer that has been accepted. For A: barcodeplot how to increase the font size
Popular Question 7 months ago, created a question with more than 1,000 views. For File format for single channel analysis of Agilent microarray data with Limma?
Popular Question 7 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Popular Question 7 months ago, created a question with more than 1,000 views. For simultaneous use of robust and weighting methods in limma
Scholar 7 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?
Popular Question 7 months ago, created a question with more than 1,000 views. For Using write.table with output from topTags [was: report a possible bug of edgeR]
Popular Question 7 months ago, created a question with more than 1,000 views. For Estimating fold change from limma 'log2FC' using lumi
Popular Question 7 months ago, created a question with more than 1,000 views. For How do I find up and down regulated genes for each contrast in LIMMA?
Scholar 7 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Appreciated 7 months ago, created a post with more than 5 votes. For A: Removing continuous covariate effects in limma analysis
Appreciated 7 months ago, created a post with more than 5 votes. For A: Volcanoplot with limma - RAW P-values or Adj.P-Values

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