User: Lluís R

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Lluís R130
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130
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European Union
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10 hours ago
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2 years ago
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l************@gmail.com

Posts by Lluís R

<prev • 65 results • page 1 of 7 • next >
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Answer: A: topGO for Gene Ontology and Gene Set enrichment
... The use of more strict p-values is up to the researcher, however, consider that if you take 0.01 as threshold, you are saying you accept 1 wrong for every 100 DEG. If you correct for multiple testing you are taking into account that each test done is related to the others (because it is taken from ...
written 15 hours ago by Lluís R130
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Comment: C: topGO: No adjacent nodes prevents BP analysis
... Which versions of topGO and org.Hs.eg.db are you using? I have used topGO several times and I have never found that error. ...
written 18 hours ago by Lluís R130
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Comment: C: Different geneset same p-values in topGO
... Probably related if I set another ontology the same GO terms (they should be different!!) and p-values are used when retrieving scores: ontology(GOdata) <- "CC" resultKS.elim3 <- runTest(GOdata, algorithm = "elim", statistic = "ks") GenTable(GOdata, resultKS.elim3) GO.ID Term Annot ...
written 1 day ago by Lluís R130
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Different geneset same p-values in topGO
... I have performed the "elim" (It happens the same with the weight01 algorithm) test in the same gene universe selecting different genes. However the p-values are the same even if different number of genes are indicated as significant for the same GO.ID. Here is a reproducible example: library("topG ...
bug topgo written 1 day ago by Lluís R130
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Comment: C: Question about WGCNA soft thresholding value
... Do you mean the SFT.R.sq column of the result returned by pickSoftThreshold isn't it? I can't think a reason how the scale free topology fit could be negative. Could you upload the image? ...
written 2 days ago by Lluís R130
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Comment: C: Problems with RSQLite compilation
... My apologies Martin, I didn't understood the error message. I couldn't provide further help than pointing that it wasn't an error due to BiocLite. ...
written 5 days ago by Lluís R130
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Comment: C: Problems with RSQLite compilation
... RSQLite is not in Bioconductor, so you don't need to use BiocLite, to install it. The problem installing RSQLite doesn't seem to be due to BiocLite. ...
written 5 days ago by Lluís R130
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Comment: C: GSA error with any ExpressionSets
... sessionInfo is a function of R which explains which is your environment in R and the version of packages you are using. You need to do: > sessionInfo() Before the line where the errors are produced ...
written 5 days ago by Lluís R130
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Comment: C: GSA error with any ExpressionSets
... Which is your sessionInfo? Did you check for NAs in your datasets `any(is.na(exprs(dataset)))`? I wouldn't expect any but there might be one or several in those data sets. ...
written 6 days ago by Lluís R130
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Comment: C: Surrogate variables affecting just one sample?
... Could you please point me where it is documented (I am sorry I missed it) ? I had to change my design matrix to include the intercept, which makes harder to perform some comparisons. Despite using intercept it didn't improve the distribution of adjusted p-values when using the surrogate variables i ...
written 7 days ago by Lluís R130

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