Showing : RNA-SEQ • reset
4
votes
3
replies
20k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 4.2 years ago by 48k • written 4.8 years ago by • 0
4
votes
8
replies
20k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 4.1 years ago by 40k • written 4.1 years ago by ▴ 20
3
votes
6
replies
18k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
6.1 years ago nikmehr22 • 0
5
votes
2
replies
17k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 20 months ago by • 0 • written 4.7 years ago by ▴ 30
19
votes
11
replies
16k
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 7.6 years ago by 48k • written 7.6 years ago by ▴ 50
14
votes
9
replies
13k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
8.7 years ago gavrielmatt ▴ 30
1
vote
14
replies
9.7k
views
DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
8.5 years ago rodriguez.varenka • 0
40
votes
44
replies
9.2k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 5.8 years ago by ▴ 60 • written 6.4 years ago by ▴ 10
2
votes
10
replies
7.9k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 7.0 years ago by 40k • written 7.0 years ago by ▴ 10
11
votes
8
replies
7.7k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.0 years ago by ★ 2.8k • written 7.0 years ago by ▴ 70
9
votes
14
replies
7.7k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
7.2 years ago • updated 7.1 years ago anand_mt ▴ 80
9
votes
11
replies
7.0k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 30
3
votes
3
replies
6.2k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 8.5 years ago by ▴ 360 • written 8.5 years ago by • 0
8
votes
2
replies
5.6k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 8.5 years ago by 40k • written 8.5 years ago by ▴ 90
1
vote
13
replies
5.6k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
7.4 years ago gil.hornung • 0
4
votes
5
replies
5.5k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 7.3 years ago by ★ 3.5k • written 7.4 years ago by ▴ 180
1
vote
8
replies
5.5k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 2.7 years ago by 40k • written 3.8 years ago by • 0
0
votes
1
reply
5.5k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 6.1 years ago by 40k • written 6.1 years ago by • 0
9
votes
11
replies
5.2k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 6.6 years ago by ▴ 20 • written 7.4 years ago by ▴ 10
10
votes
10
replies
5.2k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
5.5 years ago • updated 4.7 years ago rached ▴ 50
3
votes
7
replies
5.1k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 5.5 years ago by ▴ 30 • written 7.6 years ago by ▴ 40
4
votes
6
replies
5.1k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 11 months ago by ▴ 20 • written 5.4 years ago by ▴ 10
3
votes
4
replies
5.0k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 6.1 years ago by 40k • written 6.1 years ago by ▴ 10
2
votes
5
replies
4.9k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 20
5
votes
5
replies
4.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 4.5 years ago by 40k • written 4.5 years ago by ▴ 50
5
votes
12
replies
4.7k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 23 months ago by ▴ 30 • written 6.0 years ago by ▴ 40
0
votes
2
replies
4.6k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 7.5 years ago by 40k • written 7.5 years ago by • 0
3
votes
2
replies
4.4k
views
DESeq2 design formula with multiple factors
deseq2 RNA-Seq
updated 3.2 years ago by 40k • written 3.2 years ago by ▴ 10
3
votes
4
replies
4.4k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
6.0 years ago David Requena ▴ 20
3
votes
7
replies
3.9k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 7.5 years ago by 48k • written 7.5 years ago by ▴ 70
3
votes
2
replies
3.8k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 16 months ago by ▴ 10 • written 3.1 years ago by ▴ 80
10
votes
4
replies
3.8k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 7.2 years ago by 48k • written 7.2 years ago by ▴ 110
3
votes
12
replies
3.7k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 5.0 years ago by ★ 2.8k • written 5.0 years ago by ▴ 10
3
votes
3
replies
3.5k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 20
1
vote
5
replies
3.5k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 7.0 years ago by ★ 2.8k • written 7.0 years ago by ▴ 70
3
votes
6
replies
3.5k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 60
1
vote
1
reply
3.5k
views
WGCNA - signedKME function
WGCNA RNA-seq signedKME
updated 8.7 years ago by ★ 2.8k • written 8.7 years ago by ▴ 10
7
votes
7
replies
3.5k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 3.9 years ago by ★ 28k • written 4.0 years ago by ▴ 50
2
votes
1
reply
3.4k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 5.6 years ago by ▴ 1000 • written 5.6 years ago by ▴ 20
0
votes
2
replies
3.4k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 7.6 years ago by ★ 2.8k • written 7.6 years ago by ▴ 10
6
votes
7
replies
3.4k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 90
18
votes
12
replies
3.3k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 8.3 years ago by 40k • written 8.3 years ago by 7.8k
14
votes
9
replies
3.3k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 5.7 years ago by ▴ 130 • written 7.4 years ago by ▴ 80
0
votes
2
replies
3.3k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 18 months ago by • 0 • written 5.6 years ago by • 0
2
votes
3
replies
3.1k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
1
vote
4
replies
3.1k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 2.4 years ago by ★ 1.0k • written 6.0 years ago by • 0
12
votes
2
replies
3.1k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 7.2 years ago by 48k • written 7.3 years ago by ▴ 80
4
votes
6
replies
3.0k
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 4.6 years ago by 40k • written 4.6 years ago by ▴ 70
0
votes
3
replies
3.0k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2 StringTie RNA-seq normalisation
updated 3.8 years ago by 40k • written 3.8 years ago by • 0
9
votes
1
reply
3.0k
views
limma Time Course Experiment with many time points
limma RNA-Seq
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 130
50 results • Page 1 of 1
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Replies
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Votes
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
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