## User: nonCodingGene

Reputation:
10
Status:
New User
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Last seen:
3 months, 2 weeks ago
Joined:
4 years ago
Email:
k**********@gmail.com

#### Posts by nonCodingGene

<prev • 31 results • page 1 of 4 • next >
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... 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 3 months ago by nonCodingGene10
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... 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 ...
written 3 months ago by nonCodingGene10 • updated 3 months ago by James W. MacDonald48k
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... 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 3 months ago by nonCodingGene10
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... sum(is.na(dge$weights)) outputs 0 ... written 3 months ago by nonCodingGene10 1 answers 153 views 1 answers ... Sorry, I forgot to show that also tested for max(dge$weights) and min(dge$weights), and values where 1 and 0. ... written 3 months ago by nonCodingGene10 1 answer 153 views 1 answer ... I'm using edgeR and an error for which I have not found a solution just appeared. design <- model.matrix(~Cell.type, data = colData(summ.exp_norm)) dge$weights <- zinb.weights dge <- estimateDisp(dge, design) Error in .compressWeights(y, weights) : weights must be finite positive values ...
written 3 months ago by nonCodingGene10 • updated 3 months ago by Aaron Lun21k
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... 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 14 months ago by nonCodingGene10
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... 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 ...
written 14 months ago by nonCodingGene10 • updated 14 months ago by Gordon Smyth35k
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... The identical() test returns a FALSE, so thats is the problem. Thanks for the answer. ...
written 2.4 years ago by nonCodingGene10
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... 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" ...
written 2.4 years ago by nonCodingGene10 • updated 2.4 years ago by Martin Morgan ♦♦ 22k

#### Latest awards to nonCodingGene

Popular Question 2.4 years ago, created a question with more than 1,000 views. For AnnotatedDataFrame is not a defined class

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