Showing : RNA-Seq • reset
41
votes
44
replies
13k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.4 years ago by ▴ 60 • written 8.0 years ago by ▴ 10
10
votes
14
replies
9.7k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
8.8 years ago • updated 8.7 years ago anand_mt ▴ 90
1
vote
14
replies
11k
views
DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
10.1 years ago rodriguez.varenka • 0
1
vote
13
replies
7.1k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
9.1 years ago gil.hornung • 0
0
votes
13
replies
2.3k
views
Understanding differences in results with and without setting of pairing factor
DESeq2 deseq2 rna-seq paired samples
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 90
1
vote
12
replies
1.9k
views
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 90
18
votes
12
replies
4.4k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.9 years ago by 43k • written 9.9 years ago by ★ 7.9k
5
votes
12
replies
6.5k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 3.5 years ago by ▴ 30 • written 7.6 years ago by ▴ 40
9
votes
12
replies
8.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 12 months ago by • 0 • written 9.8 years ago by ▴ 30
15
votes
12
replies
3.1k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 60
3
votes
12
replies
6.7k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by ▴ 10
4
votes
11
replies
2.9k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 9.2 years ago by ★ 6.8k • written 9.2 years ago by ▴ 10
24
votes
11
replies
20k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom limma voom rna-seq quantile normalization
updated 9.3 years ago by 52k • written 9.3 years ago by ▴ 50
9
votes
11
replies
6.1k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 8.2 years ago by ▴ 20 • written 9.0 years ago by ▴ 10
0
votes
11
replies
2.0k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
6.1 years ago saddamhusain77 • 0
2
votes
11
replies
3.8k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
5.5 years ago • updated 5.4 years ago mico • 0
5
votes
11
replies
4.2k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
5.9 years ago • updated 5.8 years ago pierre.marin • 0
3
votes
11
replies
2.6k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 670
2
votes
10
replies
2.3k
views
Coseq error with DESeq2 object: Error in "normFactors"
coseq rna-seq
updated 6.2 years ago by ▴ 80 • written 6.2 years ago by • 0
0
votes
10
replies
2.9k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 6.1 years ago by • 0
12
votes
10
replies
8.5k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
7.1 years ago • updated 6.3 years ago rached ▴ 60
2
votes
10
replies
13k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
2
votes
10
replies
2.5k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
9.2 years ago Yogender Gowtham ▴ 20
2
votes
9
replies
2.5k
views
i can't find cummeRbund package
software error cuumeRbund rna-seq
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 40
1
vote
9
replies
2.6k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs RNA-Seq Isoforms DTU expression
updated 5.8 years ago by ▴ 20 • written 5.8 years ago by • 0
14
votes
9
replies
17k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
10.3 years ago gavrielmatt ▴ 30
5
votes
9
replies
2.7k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.8 years ago Yang Shi ▴ 10
3
votes
9
replies
2.9k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
4.4 years ago Pufall, Miles A ▴ 30
10
votes
9
replies
2.2k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom voom limma rna-seq
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
4
votes
9
replies
1.8k
views
RNA-seq analysis edgeR
rna-seq edger
updated 8.5 years ago by ★ 7.9k • written 8.5 years ago by ▴ 20
14
votes
9
replies
4.4k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 7.3 years ago by ▴ 130 • written 9.0 years ago by ▴ 80
2
votes
8
replies
2.4k
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
8
replies
3.6k
views
RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq edgeR estimatedispersions bacteria
10.2 years ago Mauve • 0
11
votes
8
replies
11k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 8.6 years ago by ★ 3.0k • written 8.6 years ago by ▴ 70
4
votes
8
replies
25k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 20
1
vote
8
replies
2.3k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq time series patient limma-voom
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 90
0
votes
8
replies
2.9k
views
Isoforms detection using bioconductor
bioconductor biomart granges rna-seq
updated 7.7 years ago by ★ 11k • written 7.7 years ago by • 0
0
votes
8
replies
2.6k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
4
votes
8
replies
1.6k
views
problem in designing matrix and batch effect
edger rna-seq matrix
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
3
votes
8
replies
4.3k
views
Normalisation in DESeq2
deseq2 rna-seq
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 10
1
vote
8
replies
10.0k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4.3 years ago by 43k • written 5.4 years ago by • 0
4
votes
8
replies
3.0k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.2 years ago by 68k • written 4.9 years ago by ▴ 30
0
votes
7
replies
2.9k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 3.5 years ago by • 0 • written 7.9 years ago by ▴ 40
2
votes
7
replies
2.5k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
8
votes
7
replies
7.3k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 5.5 years ago by ★ 28k • written 5.6 years ago by ▴ 50
3
votes
7
replies
6.3k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 7.1 years ago by ▴ 30 • written 9.2 years ago by ▴ 40
6
votes
7
replies
5.1k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 90
5
votes
7
replies
4.3k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
3
votes
7
replies
2.3k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2 twins design formula RNA-seq
7.5 years ago Simone • 0
5
votes
7
replies
3.0k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
Answer: How to formulate 2 factor nested design in DESeq2
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