Moderator: Gordon Smyth

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

Posts by Gordon Smyth

<prev • 3,163 results • page 2 of 317 • next >
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Answer: A: kegga error from edgeR
... When you run kegga() in edgeR, the de argument is supposed to be a fitted model object (DGELRT or DGEExact). Please type help("kegga.DGELRT") for documentation. You have seem to have instead input a data.frame. That will generally give an error because kegga() isn't intended to accept a data.frame. ...
written 3 days ago by Gordon Smyth32k
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Comment: C: model.matrix from GDS data
... Just remove the "-1" from the model.matrix() line and don't reset the design colnames. Then it will run correctly. The only reason for suppressing the intercept from the design matrix would be define your own contrasts. Since you haven't defined any contrasts, you shouldn't do that. ...
written 4 days ago by Gordon Smyth32k
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Answer: A: model.matrix from GDS data
... You certainly want do.log=FALSE, because (as GEO tells you) the data has been gcrma normalized and log2 transformed already. I don't see how you can be running topTreat() since you haven't run treat(). Anyway, it is certainly not true that topTreat() gives smaller p-values than topTable(). Apart f ...
written 5 days ago by Gordon Smyth32k
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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(). kegga simply reads annotation from the KEGG website. However KEGG does not provide annotation for the Trichoderma gamsii species, as you can see from their website: http://www.kegg.jp/kegg/catalog/org_list.html The closest species is Trichoderma ree ...
written 6 days 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 I ask this many published sources include gene symbols that are no longer current official symbols.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 6 days 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 6 days 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 6 days 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 10 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 10 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 10 days ago by Gordon Smyth32k

Latest awards to Gordon Smyth

Scholar 8 months ago, created an answer that has been accepted. For A: Identification of DEGs through limma analysis
Appreciated 8 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 9 months ago, created a question with more than 1,000 views. For limma: paired + multiple comparisons + technical replication?
Scholar 9 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 10 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 11 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 11 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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