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User: Ric

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Ric • 140
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140
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Australia
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an hour ago
Joined:
5 years, 8 months ago
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m*******@gmail.com

Posts by Ric

<prev • 90 results • page 1 of 9 • next >
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Comment: C: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
... Thank you for your help. Yes, I found another tutorial [here](https://bcbio.wordpress.com/2009/10/18/gene-ontology-analysis-with-python-and-bioconductor/) which took a slightly different approach. ...
written 3 days ago by Ric • 140
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Comment: C: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
... I have got `'names' attribute [44620] must be the same length as the vector [33975]` > genesOfInterest <- rownames(tr@.Data[[1]]) > head(genesOfInterest) [1] "sp0025247" "sp0025250" "sp0025268" "sp0025270" "sp0025282" "sp0056834" > indices <- c() > for (i in 1: ...
written 4 days ago by Ric • 140
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Answer: A: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
... > genesOfInterest <- rownames(tr@.Data[[1]]) > head(genesOfInterest) [1] "sp0025247" "sp0025250" "sp0025268" "sp0025270" "sp0025282" "sp0056834" > geneList <- factor(as.integer(grep(genesOfInterest, geneUniverse))) Warning message: In grep(genesOfInterest, gene ...
written 4 days ago by Ric • 140
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Comment: C: topGO allGenes argument
... It turns out that [allGenes](https://bcbio.wordpress.com/2009/10/18/gene-ontology-analysis-with-python-and-bioconductor/) should be a R vector which contains the - gene names and - p-value How to convert `tr` (1st and 5th column) to an vector? ...
written 4 days ago by Ric • 140
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Comment: C: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
... I found another tutorial [here](https://bcbio.wordpress.com/2009/10/18/gene-ontology-analysis-with-python-and-bioconductor/) but I do not know how to use it only in R ...
written 4 days ago by Ric • 140
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Comment: C: Goseq pwf nullp error
... Could you please provide an example of : - genes_list - hs.fa.len? ...
written 4 days ago by Ric • 140
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Answer: A: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
... I have followed this [tutorial](http://avrilomics.blogspot.com.au/2015/07/using-topgo-to-test-for-go-term.html) for topGO. Only thing which I changed was: ``` > genesOfInterest <- read.table("interestinggenes.txt",header=FALSE) > genesOfInterest <- as.character(genesOfInterest$V1) ``` t ...
written 4 days ago by Ric • 140
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topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
... Hi, I have got an *Error in .local(.Object, ...) : allGenes must be a factor with 2 levels* using the following code > library(edgeR) > library(topGO) ... > tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(1.5)) > topTags(tr) Coefficient: -1*Leaves.2 1*Leaves.3 ...
R topgo rna-seq edger written 5 days ago by Ric • 140
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topGO allGenes argument
... Hi, In this [paper](https://f1000research.com/articles/5-1438/v2) they used the following to determine differential expression > tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(1.5)) > topTags(tr) Coefficient: -1*Leaves.2 1*Leaves.3 logFC unshrunk.logFC logCPM PV ...
R topgo rna-seq edger written 5 days ago by Ric • 140 • updated 5 days ago by e.rempel • 430
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Comment: C: How To Get Length Data For Goseq
... Apparently, `nullp` expects a vector for bias.data, not a `data.frame`. What is the best way to convert it to a vector after I read it with `read.delim()`? ...
written 5 days ago by Ric • 140

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Scholar 3 days ago, created an answer that has been accepted. For A: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
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