Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth38k
Reputation:
38,480
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Trusted
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
16 years, 8 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 • 3,786 results • page 2 of 379 • next >
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Answer: A: Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
... No, this isn't a bug. The `estimateDisp` function is behaving as documented. > estimateDisp function clearly stats the weights argument is the numeric matrix of observation weight Please read the help page again. The help page says that `weights` is an argument for `estimateDisp` when `y` is co ...
written 8 days ago by Gordon Smyth38k
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Comment: C: Opening Illumina HT12 V3.0 Data from GEO
... OP has copied Mark Dunning's code (which was for a specific dataset) from https://support.bioconductor.org/p/70064. I reformated OP's question before, now I've removed the extra quote mark as well. ...
written 10 days ago by Gordon Smyth38k
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Answer: A: Does edgeR need to specify reference group?
... edgeR and DESeq2 are identical in the way that they define factors since both packages simply use base R functions like `factor` and `relevel`. Specifying the reference level explicitly is optional in both packages. You will find a discussion of the `relevel` function for example on pages 30, 33, 3 ...
written 10 days ago by Gordon Smyth38k
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Comment: C: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... No that is not what is happening. edgeR always gives you the DE list corresponding to the coefficient in the design matrix that you specified. In this case the coefficient is just the log-expression of a particular group, so you will get genes that are highly expressed in that group. That is why yo ...
written 10 days ago by Gordon Smyth38k
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Comment: C: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... > The data contained transcript IDs No, it doesn't. IDs starting with "ENSG" are Ensembl *gene* IDs. IDs starting with "ENST" would be Ensembl transcript IDs. > I thought that discarding the uninteresting genes will not impact the analysis. It does impact the analysis. The `eBayes` function ...
written 10 days ago by Gordon Smyth38k
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Answer: A: Variation in the estimation of the common dispersion
... By default, `estimateGLMCommonDisp()` takes a systematic sample of 10,000 rows to compute the common dispersion from. If you change the order of the genes in `y`, then the selection of genes can in some circumstances change slightly and this will change the estimated dispersion. As your post shows, ...
written 10 days ago by Gordon Smyth38k
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Answer: A: DeSeq2 Design (A-B)-(C-D)
... Well, yes, testing (A-B)-(C-D) would be routine for limma or edgeR, but DESeq2 can presumably do it as well (see Michael Love's answer). ...
written 10 days ago by Gordon Smyth38k
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Comment: C: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... Re-inforcing point 4. All expressed genes should be input to `eBayes`, not just a few genes you are interested in. If there are only a few genes of interest, then subset the fitted model object input to topTable: ``` topTable(lmfit[mysubset,], coef="Th1_vs_Nai4") ``` Note also my comments on TPMs: ...
written 11 days ago by Gordon Smyth38k
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Comment: C: How to normalize RNA-seq data if majority of transcripts expected to be differen
... It is impossible for RNA-seq to show a reduction in expression for all genes. Any global change in expression is indistinguishable from variations in sequencing depth. RNA-seq only measures relative expression within each sample. ...
written 11 days ago by Gordon Smyth38k
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Answer: A: Rsubread CIGAR output M only?
... Rsubread uses the M format. You can however get the number of mismatches from the NM ("edit distance") tag: the number of Xs is NM minus any insertions or deletions. ...
written 11 days ago by Gordon Smyth38k

Latest awards to Gordon Smyth

Scholar 8 weeks ago, created an answer that has been accepted. For A: Limma residuals matrix
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Limma residuals matrix
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 8 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 9 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 11 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 11 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 11 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 12 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 12 weeks ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Popular Question 9 months ago, created a question with more than 1,000 views. For Columns used by read.maimages for Agilent arrays
Popular Question 9 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Popular Question 9 months ago, created a question with more than 1,000 views. For non-integer counts for edgeR
Scholar 9 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
Scholar 9 months ago, created an answer that has been accepted. For A: barcodeplot how to increase the font size
Popular Question 9 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 9 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Popular Question 9 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?
Popular Question 9 months ago, created a question with more than 1,000 views. For Estimating fold change from limma 'log2FC' using lumi
Scholar 9 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 9 months ago, created a question with more than 1,000 views. For simultaneous use of robust and weighting methods in limma
Scholar 9 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?

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