The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

User: nonCodingGene

gravatar for nonCodingGene
Reputation:
10
Status:
New User
Location:
Last seen:
6 months, 3 weeks ago
Joined:
4 years, 3 months ago
Email:
k**********@gmail.com

Posts by nonCodingGene

<prev • 31 results • page 1 of 4 • next >
0
votes
1
answer
112
views
1
answers
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 7 months ago by nonCodingGene • 10
4
votes
1
answer
112
views
1
answer
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 7 months ago by nonCodingGene • 10 • updated 7 months ago by James W. MacDonald ♦ 49k
0
votes
1
answer
215
views
1
answers
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 7 months ago by nonCodingGene • 10
0
votes
1
answer
215
views
1
answers
Comment: C: weights must be finite positive value
... sum(is.na(dge$weights)) outputs 0 ...
written 7 months ago by nonCodingGene • 10
0
votes
1
answer
215
views
1
answers
Comment: C: weights must be finite positive value
... Sorry, I forgot to show that also tested for max(dge$weights) and min(dge$weights), and values where 1 and 0. ...
written 7 months ago by nonCodingGene • 10
0
votes
1
answer
215
views
1
answer
weights must be finite positive value
... I'm using edgeR and an error for which I have not found a solution just appeared. design <- model.matrix(~Cell.type, data = colData(summ.exp_norm)) dge$weights <- zinb.weights dge <- estimateDisp(dge, design) Error in .compressWeights(y, weights) : weights must be finite positive values ...
edger estimatedispersions written 7 months ago by nonCodingGene • 10 • updated 7 months ago by Aaron Lun • 22k
0
votes
1
answer
313
views
1
answers
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 17 months ago by nonCodingGene • 10
0
votes
1
answer
313
views
1
answer
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 17 months ago by nonCodingGene • 10 • updated 17 months ago by Gordon Smyth ♦ 36k
0
votes
1
answer
999
views
1
answers
Comment: C: sampleNames differ between assayData and phenoData
... The identical() test returns a FALSE, so thats is the problem. Thanks for the answer. ...
written 2.7 years ago by nonCodingGene • 10
2
votes
1
answer
999
views
1
answer
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 2.7 years ago by nonCodingGene • 10 • updated 2.7 years ago by Martin Morgan ♦♦ 23k

Latest awards to nonCodingGene

Popular Question 6 months ago, created a question with more than 1,000 views. For AnnotatedDataFrame is not a defined class
Popular Question 2.7 years ago, created a question with more than 1,000 views. For AnnotatedDataFrame is not a defined class
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 321 users visited in the last hour