Moderator: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth32k
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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:
32 minutes ago
Joined:
15 years ago
Email:
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: How to create a customized OrgDb in order to perform kegga analysis?
... You don't need an OrgDb package to run kegga. What species are you working with and what annotation were you planning to create a package from? ...
written 11 hours ago by Gordon Smyth32k
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Comment: C: Converting gene symbol list to Entrez IDs
... Where did you get the list of gene symbols from? From a published paper? I ask this many published sources include gene symbols that are no longer current official symbols. Your file has a "csv" extension, suggesting that it is a comma-separated file, but then you specify sep="/". What gives with t ...
written 17 hours ago by Gordon Smyth32k
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Comment: C: How to perform time-course differential expression with "erroneous" baseline in
... Is "innoculated" a synonym here for "infected", or do these terms mean different things? Were the control.0hai and infected.0hai samples both innoculated? For how long? If they were extracted 1 hour after infection (for example), could they be treated as 1 hour infected samples? What about control ...
written 22 hours ago by Gordon Smyth32k
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Answer: A: How to perform time-course differential expression with "erroneous" baseline in
... That certainly seems sensible to me. It is generally appropriate to correct each infection for the appropriate control, which is what your contrast seems to be doing. Just a disclaimer though: this site is really intended to advise you on correct use of the software rather than on scientific analys ...
written 22 hours ago by Gordon Smyth32k
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Comment: C: processing agilent data by limma
... No, you can't read GSM233020.txt. Sure, you get a result, but the result is wrong. As I told you in my answer, the end of that file is corrupted. ...
written 4 days ago by Gordon Smyth32k
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Answer: A: processing agilent data by limma
... The file GSM233020.txt on GEO is corrupted, and therefore can't be read correctly by limma or any other program. As James has said, all the other files for that GEO series are fine I suggest you write to the original authors of the series and ask for the correct raw data file. Alternatively, just o ...
written 4 days ago by Gordon Smyth32k
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Answer: A: File format for single channel analysis of Agilent microarray data with Limma?
... This question was answered here: https://support.bioconductor.org/p/45792/ ...
written 4 days ago by Gordon Smyth32k
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Answer: A: [goana] function within edgeR not working for Arabidopsis
... goana() requires Entrez Gene IDs and, since there is no Entrez Gene ID-based annotation package for A. Thaliana, this means that you unfortunately can't use goana() with A. Thaliani. The documentation provided by help("goana") tells you that uses goana() requires Entrez GeneIDs, and not Tair IDs. T ...
written 4 days ago by Gordon Smyth32k
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Answer: A: Using kegga and goana for Plants
... Actually, kegga() works fine with A. Thaliana. It does recognize species="At" and it does not require the org.At package. Have you read the documentation provided by help("kegga")? The error you have received tells you that you have not passed the gene IDs correctly to kegga(). If you show us the o ...
written 4 days ago by Gordon Smyth32k
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Comment: C: Trouble with Tximport for edgeR
... No, offsets are not used by exactTest(). Offsets are only used by the glm-based functions. ...
written 9 days ago by Gordon Smyth32k

Latest awards to Gordon Smyth

Scholar 7 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Appreciated 7 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Popular Question 8 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 8 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 8 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 9 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Teacher 9 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 9 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 10 months ago, created a question with more than 1,000 views. For Filtering is not recommended with LIMMA?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Confidence intervals on edgeR logFC
Scholar 10 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Appreciated 10 months ago, created a post with more than 5 votes. For BH vs BY in p.adjust + FDR interpretation
Scholar 10 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Popular Question 10 months ago, created a question with more than 1,000 views. For total count filter cutoff (edgeR)
Commentator 10 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 10 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 11 months ago, created an answer with at least 3 up-votes. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 11 months ago, created an answer that has been accepted. 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: seeking a paper or journal review about repeated multiple testing for Biological
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: limma; Only fit list of certain genes/ filter eSet
Scholar 11 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet
Scholar 11 months ago, created an answer that has been accepted. For A: limma; Only fit list of certain genes/ filter eSet

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