Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth32k
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31,730
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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:
4 hours ago
Joined:
14 years, 9 months ago
Email:
s****@wehi.edu.au

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

Posts by Gordon Smyth

<prev • 3,062 results • page 1 of 307 • next >
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Answer: A: Using limma analyze raw data of illumina beadchip
... Unfortunately the researchers who deposited GSE93219 chose to upload their data in a rather minimalistic form. They uploaded a matrix of (background corrected) intensity values but nothing else. They didn't upload IDAT files, detection p-values or control probe information. Unfortunately this means ...
written 3 days ago by Gordon Smyth32k
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Answer: A: No annotated genes found in universe error using goana and kegga
... You haven't correctly passed the gene Ids to kegga. Where are your gene IDs stored? By default, kegga() will look in rownames(lrt) for the gene Ids. But if you have stored them in a column of x$genes, then you have to tell kegga() in which column to look. Note that org.Dm.eg.dg is not relevant her ...
written 6 days ago by Gordon Smyth32k
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Comment: C: Anova test on gene expression data
... Is there any reason why you don't want to use the Bioconductor packages designed to do this? ...
written 7 days ago by Gordon Smyth32k
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Comment: C: Two-way anova 2x2 design with limma
... You should read the limma User's Guide that comes with the version of the limma package you are using. Or else the latest version of the Guide is always available from: https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf Your reference to Section 8.7 suggests tha ...
written 8 days ago by Gordon Smyth32k
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Answer: A: RNASeq interaction between factors with edgeR when cpms tend to zero
... Yes, the reason is the zero counts. As Aaron has already explained, fold-changes are indeterminate when the counts are zero. This is a universal statistical issue, not particular to edgeR. You can see the issue clearly from a Fisher exact test. Suppose the counts for a particular gene are as follow ...
written 9 days ago by Gordon Smyth32k
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Answer: A: limma wsva() does not return what it says it will
... Thanks for letting me know. The help page is now updated. (Earlier versions of the function did output the whole augmented design matrix instead of just the surrogate variables.) ...
written 12 days ago by Gordon Smyth32k
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Answer: A: Strong upwards correlation between log fold change and average log expression in
... Just to reinforce James' answer, the problem is that you haven't actually computed any log-fold-changes yet. So you're just plotting one mean against another. Why did you include the "0+" in your model? Presumably you got that from reading a suggested analysis somewhere. If so, then go back to to t ...
written 12 days ago by Gordon Smyth32k
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Comment: C: Pathway analysis from list of differentially expressed genes with fold change, p
... How long a list of genes do you have? Do you have just a short list of DE genes or do you have p-values and logFCs for a whole microarray (say)? ...
written 12 days ago by Gordon Smyth32k
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Comment: C: mas5 normalisation giving negetive value after using exprs()
... My apologies, you're correct. I had assumed that all normalization functions in the affy package produced results on the log scale in order to be consistent. ...
written 16 days ago by Gordon Smyth32k
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Comment: C: No genes found in universe : goana error
... Yes, goana needs to know where to find the Entrez Gene IDs, so you have to tell it the column name. By default it tries to use the row names which, in this case, aren't the right IDs. ...
written 17 days ago by Gordon Smyth32k

Latest awards to Gordon Smyth

Scholar 4 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Appreciated 4 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Popular Question 5 months ago, created a question with more than 1,000 views. For Limma - RNA-Seq DE genes - Quantile normalized log transformed RPKM data
Popular Question 6 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 6 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 6 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tes
Teacher 7 months 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 7 months ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Scholar 7 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 7 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 7 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 7 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 7 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 7 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 8 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 8 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 8 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 8 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 8 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 8 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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