Showing : RNA-seq • reset
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
4
votes
8
replies
24k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
4
votes
3
replies
24k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 5.4 years ago by 52k • written 6.0 years ago by • 0
3
votes
6
replies
22k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
7.4 years ago nikmehr22 • 0
24
votes
11
replies
19k
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 8.9 years ago by 52k • written 8.9 years ago by ▴ 50
14
votes
9
replies
16k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
9.9 years ago gavrielmatt ▴ 30
41
votes
44
replies
12k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.0 years ago by ▴ 60 • written 7.6 years ago by ▴ 10
2
votes
10
replies
11k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 8.2 years ago by 43k • written 8.2 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
9.7 years ago rodriguez.varenka • 0
11
votes
8
replies
9.8k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 70
10
votes
14
replies
9.2k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
8.4 years ago • updated 8.3 years ago anand_mt ▴ 90
1
vote
8
replies
8.9k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4.0 years ago by 43k • written 5.0 years ago by • 0
9
votes
12
replies
8.6k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 7 months ago by • 0 • written 9.4 years ago by ▴ 30
12
votes
10
replies
7.8k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
6.7 years ago • updated 5.9 years ago rached ▴ 60
3
votes
3
replies
7.4k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.8 years ago by ▴ 370 • written 9.8 years ago by • 0
5
votes
5
replies
7.0k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 60
6
votes
6
replies
6.9k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 2.2 years ago by ▴ 200 • written 6.6 years ago by ▴ 10
2
votes
5
replies
6.7k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 20
1
vote
13
replies
6.7k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
8.7 years ago gil.hornung • 0
0
votes
1
reply
6.5k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
4
votes
5
replies
6.5k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 8.6 years ago by ★ 3.6k • written 8.6 years ago by ▴ 180
3
votes
2
replies
6.4k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 2.6 years ago by ▴ 10 • written 4.3 years ago by ▴ 80
8
votes
7
replies
6.2k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
8
votes
2
replies
6.2k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 90
5
votes
12
replies
6.2k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 3.1 years ago by ▴ 30 • written 7.2 years ago by ▴ 40
3
votes
7
replies
6.0k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 6.7 years ago by ▴ 30 • written 8.8 years ago by ▴ 40
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.8 years ago by ▴ 20 • written 8.7 years ago by ▴ 10
3
votes
2
replies
5.9k
views
DESeq2 design formula with multiple factors
deseq2 RNA-Seq
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 10
3
votes
4
replies
5.7k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
3
votes
12
replies
5.6k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by ▴ 10
3
votes
4
replies
5.5k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
7.2 years ago David Requena ▴ 20
0
votes
2
replies
5.0k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
10
votes
4
replies
4.9k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 8.4 years ago by 52k • written 8.4 years ago by ▴ 110
3
votes
3
replies
4.9k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 7.3 years ago by 21k • written 7.3 years ago by ▴ 20
0
votes
2
replies
4.9k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by ▴ 10
3
votes
7
replies
4.7k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 8.7 years ago by 52k • written 8.7 years ago by ▴ 90
1
vote
5
replies
4.6k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 70
0
votes
5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.6k • written 3.7 years ago by • 0
2
votes
1
reply
4.6k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 6.9 years ago by ▴ 1000 • written 6.9 years ago by ▴ 20
6
votes
7
replies
4.5k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 90
1
vote
4
replies
4.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.6 years ago by ★ 1.1k • written 7.2 years ago by • 0
14
votes
9
replies
4.2k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 6.9 years ago by ▴ 130 • written 8.6 years ago by ▴ 80
0
votes
2
replies
4.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.4 years ago by ▴ 80
3
votes
6
replies
4.1k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 9.4 years ago by 52k • written 9.5 years ago by ▴ 60
18
votes
12
replies
4.1k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.5 years ago by 43k • written 9.5 years ago by ★ 7.9k
4
votes
6
replies
4.0k
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 5.8 years ago by 43k • written 5.8 years ago by ▴ 70
5
votes
7
replies
4.0k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
0
votes
2
replies
4.0k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.8 years ago by • 0 • written 6.8 years ago by • 0
1
vote
1
reply
4.0k
views
WGCNA - signedKME function
WGCNA RNA-seq signedKME
updated 9.9 years ago by ★ 3.0k • written 9.9 years ago by ▴ 10
3
votes
3
replies
4.0k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.7 years ago by ▴ 30 • written 5.9 years ago by ▴ 40
50 results • Page 1 of 1
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Replies
Comment: Cannot install GO.db and org.Hs.eg.db by Gabriel • 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Answer: Feature Counts -R XS Read Assignment Tag by Gordon Smyth 52k
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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