Moderator: Gordon Smyth

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Gordon Smyth31k
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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
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9 hours ago
Joined:
14 years, 7 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

<prev • 2,989 results • page 1 of 299 • next >
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Answer: A: differentially expressed genes form RSEM genes data
... Non-integer counts are no problem, see: https://support.bioconductor.org/p/100516 ...
written 1 day ago by Gordon Smyth31k
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Answer: A: limma: Camera() about the input data
... In general, camera() can be run on log-expression data, as would be used for any differential expression analysis. I can't comment specifically on data that you may have downloaded from the TCGA. I don't know what you mean by a "Z-score function" but it doesn't sound like anything you would need or ...
written 1 day ago by Gordon Smyth31k
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Comment: C: Volcano Plot after using Treat Function
... OK, I see. I wish you'd mentioned this in your original question. Anyway you are right, volcanoplot() is not currently working with treat(). ...
written 3 days ago by Gordon Smyth31k
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Answer: A: RNA-Seq DEG analysis questions
... My advice would be to analyse the blood samples and the fibroblast samples separately. Then the comparison of the proband with the control samples is a simple two-group comparison (n=1 proband vs n=3 controls). Any of the usual packages limma, edgeR or DESeq2 would be able to do the DE analysis easi ...
written 3 days ago by Gordon Smyth31k
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Answer: A: Volcano Plot after using Treat Function
... Your question has made me realize that the volcanoplot() function doesn't currently work with treat(). There's no good reason why it shouldn't, so I'll commit a fix. Note, the fact that p-values and logFCs give different rankings isn't the problem. If p-values and logFC ranked genes in the same ord ...
written 3 days ago by Gordon Smyth31k
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Answer: A: Does edgeR accept decimal / integer read counts for differential expression ?
... Yes it does. All the edgeR analysis pipelines accept fractional counts. edgeR uses a continuous version of the negative binomial distribution so that it can work directly with fractional counts without rounding them to integers. ...
written 4 days ago by Gordon Smyth31k
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Answer: A: Filtering replicated genes
... Why do you need to filter probes from you data? There is no need to filter duplicate UniProt IDs for a standard differential expression analysis. Unless you have a strong need to remove duplicate probes (and you don't mention any reason), just don't do it. Simpler is usually better. ...
written 4 days ago by Gordon Smyth31k
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Answer: A: TREAT function - how to interpret the result
... Please do not reorder the genes by fold change. The genes have already been ordered by likely biological importance according to the treat approach. Fold change is not the only consideration when judging significance or importance. One also has to take into account the consistency of the results ac ...
written 4 days ago by Gordon Smyth31k
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Answer: A: Choosing genes for clustering
... Your question assumes that there is some trick to choosing DE genes, but really there isn't. By definition, the DE analysis is choosing the genes that best separate the two groups. So the best set of DE genes to separate the two sample groups are just the top DE genes. The top gene separates the gro ...
written 5 days ago by Gordon Smyth31k
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Comment: C: Selecting genes that best separate between two groups
... In my opinion there is no good way to conduct a DE analysis of TPM values from Kallisto. TPM values throw away too much information that DE software needs to know. I would be surprised though if that is the entire source of the problem.   ...
written 5 days ago by Gordon Smyth31k

Latest awards to Gordon Smyth

Scholar 12 weeks ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Appreciated 12 weeks ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Popular Question 3 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 4 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 4 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 4 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 4 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 5 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 5 months ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Scholar 5 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 5 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 5 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 5 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 5 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 5 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 6 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 6 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 6 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 6 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 6 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 6 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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