User: peirinl

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peirinl0
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Posts by peirinl

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How to plot the top_GO result using GOplot?
... I run my gene ontology enrichment analysis using topGO. Now I wish to use GOplot to plot the figure. But I see one of the required columns are adj P value, which is not found in my result. How can I add the adj P value result in my top_GO result?  By the way, why the Rank in fisher.classic is not c ...
topgo goplot written 6 days ago by peirinl0
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Problem in genelist levels when running topGO.
... I am running multi-level experiment of a dataset using LIMMA, contrast_matrix_Grade<- makeContrasts(AdvanceVsEarlyinT = A.T-nA.T,                                       AdvanceVsEarlyinnT = A.nT-nA.nT,                                        TVsnTinAdvance = A.T-A.nT, TVsnTinEarly = nA.T-nA.nT,   ...
topgo written 11 days ago by peirinl0
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Comment: C: Error in last step of Limma analysis (eBayes)
... Ok. I modified i <- pData(eset)$Sample_title into this:  i <- sub("-.*", "", pData(eset)$Sample_title), then the data become as what i show up there. ...
written 11 days ago by peirinl0
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Comment: C: Error in last step of Limma analysis (eBayes)
... Sorry for wasting your time, but I make a stupid mistake.  HighVsLowinnT = H.nT-H.nT     should be     HighVsLowinnT = H.nT-nH.nT. Thank you for helping me.  ...
written 11 days ago by peirinl0
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Answer: A: Error in last step of Limma analysis (eBayes)
... Sorry, I think I make a huge STUPID mistake.  contrast_matrix_Grade<- makeContrasts(HighVsLowinT = H.T-nH.T, HighVsLowinnT = H.nT-H.nT,                                        TVsnTinHigh = H.T-H.nT, TVsnTinLow = nH.T-nH.nT,                                       levels = design_Grade)   should ...
written 11 days ago by peirinl0
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Comment: C: Error in last step of Limma analysis (eBayes)
... The pData is here. Not sure if this work out.  https://www.dropbox.com/s/35hqpm11umynx19/eset.txt?dl=0 Sample_title, i, is the subject name i  [1] "E005" "E005" "E012" "E012" "E021" "E021" "E028" "E028" "E033" "E033" "E041" "E041" "E042" "E042" [15] "E045" "E045" "E048" "E048" "E052" "E052" "E058 ...
written 11 days ago by peirinl0
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Error in last step of Limma analysis (eBayes)
... A running limma analysis of a dataset, and I got an error in the final step, eBayes(fit2) This is my code i <- pData(eset)$Sample_title Part <- ifelse(pData(eset)$Part == "Tn", "nT", "T") Grade <- ifelse(pData(eset)$Grade == "Low", "nH", "H") sample_byGrade <- factor(paste(Grade, Part, ...
limma ebayes written 11 days ago by peirinl0
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Comment: C: Which annotationData package should I use?
... I am not sure if this is useful, but since I am using array express, there is an array_design file, A-GEOD-15048.adf.txt. Can I use this for annotation? ...
written 12 days ago by peirinl0
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Which annotationData package should I use?
... I wanna analyze dataset produce by Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray, which annotationData package should I use? ...
annotationdata rosetta/merck human rsta custom affymetrix 2.0 microarray written 14 days ago by peirinl0 • updated 14 days ago by James W. MacDonald44k
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Comment: C: Error when restore rownames of Feature data of ExpressionSet
... > anno_riester %>% filter(PROBEID=="227320_at") PROBEID SYMBOL GENENAME 1 227320_at RFLNA ZNF664-RFLNA readthrough 2 227320_at RFLNA refilin A > probe_stats %>% filter(PROBEID=="227320_at") # A tibble: 0 x 2 # ... with 2 variables: PROBEID <chr&g ...
written 17 days ago by peirinl0 • updated 17 days ago by Martin Morgan ♦♦ 20k

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