Moderator: Gordon Smyth

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Gordon Smyth30k
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Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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http://www.statsci.org...
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Google Scholar Page
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an hour ago
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14 years, 5 months ago
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s****@wehi.edu.au

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

Posts by Gordon Smyth

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Answer: A: reading text file in R
... You haven't shown us the first few lines of your file, but I will take a wild guess that if you use: my_data <- read.delim("Chr.txt", header=FALSE, sep="\t", stringsAsFactors=FALSE) you will find that it reads the file like you expect. You're getting confused at the moment (1) because the Chr ...
written 3 hours ago by Gordon Smyth30k
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Comment: C: Limma: how to get same output as topTable but for all the genes ?
... The as.data.frame(fit) call mentioned in the help file snippet does collate results for all coefficients in one data frame. ...
written 8 hours ago by Gordon Smyth30k
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Answer: A: Limma: how to get same output as topTable but for all the genes ?
... Actually, topTable() has always been able to output results for all genes if necessary. As Jenny, points out, you could simply use: tab <- topTable(fit, n=Inf, coef=2) to get results for all genes for coefficient 2. If you wanted to create a data.frame with results for all coefficients, you c ...
written 10 hours ago by Gordon Smyth30k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... OK, now you have 2 DE genes. The adjusted p-value represents false discovery rate FDR, and you have 2 genes that are significantly DE at FDR < 0.05. To see which genes these are, please use head(tab). Don't use subset -- there's just no point in that because topTable has already ranked the most i ...
written 3 days ago by Gordon Smyth30k
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Answer: A: Does DEseq2 analysis make GOseq redundant?
... Gene length bias (in an enrichment analysis) and RNA-seq normalization (variance stabilization or otherwise) are quite different things. Normalization doesn't prevent gene length bias, in fact quite the opposite. DE analysis when done properly will always show a gene length bias because longer gene ...
written 3 days ago by Gordon Smyth30k
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Comment: C: EdgeR model not of full rank
... Sorry, you're right. My suggestion to remove the all-zero columns was too simple, as it removes only 5 columns instead of 6. As Aaron has pointed out, you can still fix the design matrix yourself, but this is overly complicated and prone to error. I have edited my answer to correct it. ...
written 3 days ago by Gordon Smyth30k
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Comment: C: EdgeR model not of full tank
... One can still represent the lines in two stages: phenotype first, then line within phenotype. The model.matrix() function doesn't make that easy though -- see my answer. ...
written 4 days ago by Gordon Smyth30k
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Answer: A: EdgeR model not of full tank
... The problem here is an idiosyncracy of the model.matrix() function in R. When you try to nest one factor within another, it assumes that the levels of the nested factor start from scratch within each level of the higher factor. In your case, model.matrix() is creating extra column of 0s for each lin ...
written 4 days ago by Gordon Smyth30k
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Answer: A: Question about decideTests function and adj.p.value in "limma" R Package
... You should not use voom() together with eBayes(trend=TRUE). You should use one or the other, but not both (as explained in Chapter 15 of the limma User's Guide). Apart from that, I don't see any clear problems. You just don't have any differential expression. There's no contradiction in the results ...
written 5 days ago by Gordon Smyth30k
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Comment: C: Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
... I chose to keep the smallest Entrez Gene ID for each gene because IDs for Gene Models are larger than IDs for more established genes. From what you say, I should instead keep the mappings in the original order, so as to get the Entrez ID with best alignment for each transcript-cluster ID. I have ed ...
written 5 days ago by Gordon Smyth30k

Latest awards to Gordon Smyth

Scholar 27 days ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Appreciated 27 days ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Limma - RNA-Seq DE genes - Quantile normalized log transformed RPKM data
Popular Question 8 weeks ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 8 weeks ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 10 weeks ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
Popular Question 3 months ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Scholar 3 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 3 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 3 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 3 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 4 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 4 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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 4 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 4 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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