Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth39k
Reputation:
38,820
Status:
Trusted
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Website:
http://www.statsci.org...
Scholar ID:
Google Scholar Page
Last seen:
5 minutes ago
Joined:
16 years, 10 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 • 3,822 results • page 1 of 383 • next >
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Answer: A: model matrix in limma
... See Section 9.2 of the limma User's Guide. In R, `~0` and `~-1` are the same thing while `~1` is superfluous and possibly an error in whatever tutorial you have read. ...
written 12 hours ago by Gordon Smyth39k
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Comment: C: Nested Random Effect in LIMMA: Is It Possible?
... Just pick one level (either Lineage or Cell Line) to be the random effect, whichever is the most important. Try both perhaps and choose the one with the largest intrablock correlation. ...
written 5 days ago by Gordon Smyth39k
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Comment: C: Understanding voom behavior when model matrix is used with/without intercept for
... A first step would be to look at the design matrix and count how many columns it has. Does the number of columns change when you add `0+`? A second step would be to do a Google search for "regression through the origin". It still seems strange to me that you are devoting so much attention to this ...
written 8 days ago by Gordon Smyth39k
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Answer: A: Understanding voom behavior when model matrix is used with/without intercept for
... > Why is there a dramatic difference in the voom output when no intercept model is used? Why would you not expect a dramatic difference in the output, considering that you have made such a dramatic change to the input? It would be easier to answer your question more meaningfully if you explaine ...
written 8 days ago by Gordon Smyth39k
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Comment: C: Understanding voom behavior when model matrix is used with/without intercept for
... That's right. A nonsense design matrix will produce nonsense fitted values, and hence nonsense residuals, nonsense variances and a nonsense voom trend. OP hasn't given any explanation for why they would contemplate fitting a regression through the origin, so I don't feel obliged to write at length ...
written 8 days ago by Gordon Smyth39k
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Answer: A: Nested Random Effect in LIMMA: Is It Possible?
... No, limma does not fit nested random effects. It allows only one randomized block. ...
written 9 days ago by Gordon Smyth39k
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Comment: C: How to do DEGs based on CPM
... Yes, that is true. I will add the `trend = TRUE`. ...
written 9 days ago by Gordon Smyth39k
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Answer: A: How to do DEGs based on CPM
... See limma User's Guide, Section 15.4. ...
written 10 days ago by Gordon Smyth39k
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Answer: A: Confusion about Design Matrix ,Contrast Matrix and logFC values in limma package
... The first problem is that you are apparently trying to analyse expression data that is unlogged and (possibly) unnormalized. limma works on log2-expression values, which yours are not. Apart from that, your analysis might be ok but you are including quite a few unnecessary commands and steps. Why d ...
written 11 days ago by Gordon Smyth39k
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Comment: C: error in (function (classes, fdef, mtable) unable to find an inherited method f
... I added formatting to your post so that it is readable. Also note that you are asking a question rather than providing a tutorial. ...
written 16 days ago by Gordon Smyth39k

Latest awards to Gordon Smyth

Scholar 4 months ago, created an answer that has been accepted. For A: Limma residuals matrix
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Limma residuals matrix
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 4 months ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 months ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 months ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 months ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 months ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Scholar 4 months ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Scholar 4 months ago, created an answer that has been accepted. For A: Rsubread, Error in featureCounts paired end
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rsubread, Error in featureCounts paired end
Popular Question 11 months ago, created a question with more than 1,000 views. For Columns used by read.maimages for Agilent arrays
Popular Question 11 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Popular Question 11 months ago, created a question with more than 1,000 views. For non-integer counts for edgeR
Scholar 11 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 11 months ago, created an answer that has been accepted. For A: barcodeplot how to increase the font size
Popular Question 11 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 11 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Popular Question 11 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 11 months ago, created a question with more than 1,000 views. For Estimating fold change from limma 'log2FC' using lumi
Scholar 11 months ago, created an answer that has been accepted. For A: ANOVA-like test via treat() in limma
Popular Question 11 months ago, created a question with more than 1,000 views. For simultaneous use of robust and weighting methods in limma
Scholar 11 months ago, created an answer that has been accepted. For A: How barcode-plot enrichment is calculated?

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