Moderator: Gordon Smyth

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Gordon Smyth33k
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Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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http://www.statsci.org...
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Head of Bioinformatics Division at the Walter and Eliza Hall Institute of Medical Research

Posts by Gordon Smyth

<prev • 3,276 results • page 2 of 328 • next >
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Comment: C: edgeR for continuous independent variables
... It is not correct to batch correct expression data before using limma. As always, the batch effects or surrogate variables need to be included in the linear model rather than "removed" ahead of time. See for example: https://support.bioconductor.org/p/36029/ The problem isn't with negative values t ...
written 8 days ago by Gordon Smyth33k
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Comment: C: edgeR for continuous independent variables
... I agree that sva or RUVseq could be used to search for hidden batch effects, but ycding is only asking about a known batch factor (month) in Question 2. To handle a known factor like that, I think just including it in the design matrix would be simple and good. ...
written 9 days ago by Gordon Smyth33k
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Answer: A: edgeR for continuous independent variables
... Question 2: It is not correct or necessary to use the sva package here. Not correct because sva is not designed for use with counts. Not necessary because you know what the batches are already. If you find that there is a batch effect, just include batch as a factor in the design matrix, then edgeR ...
written 9 days ago by Gordon Smyth33k
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Answer: A: The error when using beadarry and limma packages for analysing illumina chip
... There are lots and lots of problems with your code. Many of the code steps that you give would give errors. For example, as(gse, "ExpressionSetIllumina") will fail because this is no method for coercing an ExpressionSet into an ExpressionSetIllumina (nor is there any need to convert the object an ...
written 10 days ago by Gordon Smyth33k
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Answer: A: goseq with hypergeometric method
... I am quite puzzled by your post. The goseq function seems to have run correctly both with and without gene length correction. What then is the problem? Why are you surprised that you get the same number of GO terms with and without gene length correction? Why is that a problem? You might get more o ...
written 11 days ago by Gordon Smyth33k
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Answer: A: Why does backgroundCorrect with method="none" produce different plots with plotM
... I'll add a little more detail to James' answer. When you made an MA plot (using plotMA or plotMD), the EListRaw object has to be converted first into an EList object on the log-scale in order to make the plot. So some form of background correction and normalization has to be applied. If you haven't ...
written 13 days ago by Gordon Smyth33k
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Answer: A: Up/Down Regulated GeneList from edgeR and R
... Well, there are a million ways to separate up from down genes in R. Let's assume your DE test results are stored in res. For example, if you are following the edgeR workflow, then you would have run: res <- glmQLFTest(fit, contrast=B.LvsP) Just using topTags Now you can get a table of the top ...
written 13 days ago by Gordon Smyth33k
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Answer: A: scaling data for clustering heat map
... The term "z scale" is seldom used in statistics but, when it is, it means the same as "z score". In the edgeR tutorial, you can also use coolmap(logCPM) which does most of the work for you. It will automatically standardize the expression values, so you don't need to do that yourself before hand ...
written 17 days ago by Gordon Smyth33k
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Answer: A: Agilent description of headers
... Code is already available to parse the headers for you. Just use: library(limma) x <- read.maimages(files, source="agilent") where 'files' is a vector of file names for the files you downloaded from GEO. This will read the relevant columns from all the files into a matrix-like data object tha ...
written 17 days ago by Gordon Smyth33k
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Answer: A: How to get the ordinary t statistic for two paired groups?
... I suggest that you look more closely at the output from your simulation. When I run your simulation, your limma ordinary t-test and your t-test code return identical p-values, confirming that the two approaches are in fact identical. It's generally a good idea to include the output from code with y ...
written 21 days ago by Gordon Smyth33k

Latest awards to Gordon Smyth

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Analysis of pathways using edgeR
Scholar 4 weeks ago, created an answer that has been accepted. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to plot MD plot in limma
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
Scholar 4 weeks ago, created an answer that has been accepted. For A: another contrast question - edgeR + scRNA-seq + timecourse
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: RNA-Seq, generate batch-free count matrix
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please share me your helpful comments with edgeR analysis without replicate
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Do the outputs of Limma's competitive gene set methods (camera, romer) require a
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: using duplicateCorrelation with limma+voom for RNA-seq data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Differential expression of RNA-seq data using limma and voom()
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Test whether expression levels of two gene sets are significantly different
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Diffbind: edgeR or DESeq2 ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: how to use "non-standard" species for KEGG / GO analysis in limma?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Fit a multinomial to RNA-seq count data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: vooma lm.fit versus voom lmFit
Teacher 11 months ago, created an answer with at least 3 up-votes. For Differences between limma voom E values and edgeR cpm values?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Differences between edgeR's and limma+voom's implementation of camera/roast/rome
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: seeking a paper or journal review about repeated multiple testing for Biological
Student 11 months ago, asked a question with at least 3 up-votes. For non-integer counts for edgeR

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