Showing : RNA-Seq • reset
5
votes
3
replies
28k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.3 years ago by ▴ 30
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
4
votes
3
replies
25k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 5.8 years ago by 52k • written 6.4 years ago by • 0
3
votes
6
replies
23k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
7.7 years ago nikmehr22 • 0
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
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
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
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
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
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
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
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
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
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
5
votes
5
replies
7.9k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 60
3
votes
3
replies
7.8k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.1 years ago by ▴ 370 • written 10.1 years ago by • 0
6
votes
6
replies
7.6k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 2.5 years ago by ▴ 200 • written 7.0 years ago by ▴ 10
2
votes
5
replies
7.4k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
3
votes
3
replies
7.4k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 16 days ago by • 0 • written 4.7 years ago by ▴ 80
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
3
replies
7.1k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 7.7 years ago by 21k • written 7.7 years ago by ▴ 20
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
1
reply
6.8k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
4
votes
5
replies
6.7k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 8.9 years ago by ★ 3.6k • written 9.0 years ago by ▴ 180
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
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
3
votes
2
replies
6.4k
views
DESeq2 design formula with multiple factors
deseq2 RNA-Seq
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
8
votes
2
replies
6.4k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 10.1 years ago by 43k • written 10.1 years ago by ▴ 90
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
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
3
votes
4
replies
5.9k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
3
votes
4
replies
5.7k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
7.6 years ago David Requena ▴ 20
0
votes
2
replies
5.5k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 9.2 years ago by ★ 3.0k • written 9.2 years ago by ▴ 10
0
votes
5
replies
5.4k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
10
votes
4
replies
5.3k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 8.8 years ago by 52k • written 8.8 years ago by ▴ 110
0
votes
2
replies
5.2k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 9.1 years ago by 43k • written 9.1 years ago by • 0
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
1
vote
5
replies
5.0k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 8.6 years ago by ★ 3.0k • written 8.6 years ago by ▴ 70
3
votes
7
replies
4.9k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 9.1 years ago by 52k • written 9.1 years ago by ▴ 90
2
votes
1
reply
4.9k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 7.2 years ago by ▴ 1000 • written 7.2 years ago by ▴ 20
1
vote
4
replies
4.7k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.0 years ago by ★ 1.1k • written 7.6 years ago by • 0
0
votes
2
replies
4.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.8 years ago by ▴ 80
4
votes
6
replies
4.5k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 4.9 years ago by 52k • written 4.9 years ago by ▴ 10
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
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
3
votes
3
replies
4.4k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.1 years ago by ▴ 30 • written 6.3 years ago by ▴ 40
3
votes
6
replies
4.3k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 9.8 years ago by 52k • written 9.8 years ago by ▴ 60
2
votes
3
replies
4.3k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 19 months ago by 52k • written 19 months ago by • 0
4
votes
6
replies
4.3k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 70
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
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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