User: nonCodingGene

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Posts by nonCodingGene

<prev • 31 results • page 1 of 4 • next >
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Comment: C: edgeR coefficients for DEG analysis
... To me I think the two first ways of doing the analysis are the right ones, but I do not understand what the last two comparison mean, so this confuses my a little bit. ~1+Cell.type+Patient coef = 2 ~0+Cell.type+Patient contrast = c(-1,1,0,0,0,0,0,0) ~0+Cell.type+Patient coef = 2 ~1+Cell.typ ...
written 15 months ago by nonCodingGene • 10
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edgeR coefficients for DEG analysis
... I'm trying to perform a DEG analysis of two cell types extracted from 8 different patients (data comes from scRNA). I'm trying to compare the two cells while adjusting for the patients, there are two possible models: a) ~0+cell.type+patients b) ~cell.type.patients lrt <- glmWeightedF(fit, co ...
edger written 15 months ago by nonCodingGene • 10 • updated 15 months ago by James W. MacDonald ♦ 51k
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Comment: C: weights must be finite positive value
... What can be the source of this and how can I solve it? I'm using edgeR for scRNA-seq, in order to manage droputs I use zinbwave Just in case I've checked whether one condition has a gene for which its counts are all 0, and this does not happens. This is how I calculate weights: zinb <- zinb ...
written 15 months ago by nonCodingGene • 10
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Comment: C: weights must be finite positive value
... sum(is.na(dge$weights)) outputs 0 ...
written 15 months ago by nonCodingGene • 10
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Comment: C: weights must be finite positive value
... Sorry, I forgot to show that also tested for max(dge$weights) and min(dge$weights), and values where 1 and 0. ...
written 15 months ago by nonCodingGene • 10
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weights must be finite positive value
... I'm using edgeR and an error for which I have not found a solution just appeared. design <- model.matrix(~Cell.type, data = colData(summ.exp_norm)) dge$weights <- zinb.weights dge <- estimateDisp(dge, design) Error in .compressWeights(y, weights) : weights must be finite positive values ...
edger estimatedispersions written 15 months ago by nonCodingGene • 10 • updated 15 months ago by Aaron Lun • 25k
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Comment: A: Limma RNAseq comparison with Cuffdiff
... Update, I've modify the classes vector such classes <- factor(c("NEG","NEG","NEG", "MDK","MDK","MDK"), as.character(c("NEG", "MDK"))) Now logFC are quite close to the ones obtained in cuffdiff but none of the top 7 significant genes from cuffdiff are significant in limma. 3157 significant gen ...
written 2.1 years ago by nonCodingGene • 10
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Limma RNAseq comparison with Cuffdiff
... I've the output of a differential expression analysis for RNA done with cuffdiff and I'm trying to check it with limma but I'm not getting the results that I would expect. w164 <- read.table("COUNTfile.txt", header = T, row.names = 1) head(w164) WM164_NEG_1 WM164_NEG_2 WM164_NEG_3 W ...
limma written 2.1 years ago by nonCodingGene • 10 • updated 2.1 years ago by Gordon Smyth ♦ 39k
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Comment: C: sampleNames differ between assayData and phenoData
... The identical() test returns a FALSE, so thats is the problem. Thanks for the answer. ...
written 3.3 years ago by nonCodingGene • 10
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sampleNames differ between assayData and phenoData
... Sorry for this question, but for some reason something is happening that I'm not able to find. I'm having the next problem while creating the expression set.     pd <- data.frame(state = colnames(q@mat)) rownames(pd) <- pd[,1] pd[,1] <- 1 pheno = new("AnnotatedDataFrame" ...
expresionset written 3.3 years ago by nonCodingGene • 10 • updated 3.3 years ago by Martin Morgan ♦♦ 23k

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Popular Question 14 months ago, created a question with more than 1,000 views. For AnnotatedDataFrame is not a defined class
Popular Question 14 months ago, created a question with more than 1,000 views. For loadGSC() Piano package
Popular Question 14 months ago, created a question with more than 1,000 views. For AnnotatedDataFrame is not a defined class
Popular Question 3.3 years ago, created a question with more than 1,000 views. For AnnotatedDataFrame is not a defined class
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