Showing : RNASeqData • reset
3
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6
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1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 8 weeks ago by • 0
0
votes
2
replies
509
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 6 weeks ago by • 0 • written 4 months ago by • 0
3
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13
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2.3k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 15 months ago by • 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 7 months ago by ▴ 20
0
votes
1
reply
806
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
1
vote
1
reply
481
views
Merging annotation with differential expression output
annotation RNASeqData
updated 9 months ago by 68k • written 9 months ago by • 0
0
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3
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1.1k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
389
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
11 months ago cftattersfield • 0
0
votes
5
replies
795
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
0
votes
1
reply
521
views
Correlation between gene clusters
genomes RNASeqData
written 12 months ago by • 0
0
votes
2
replies
787
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
12 months ago gingergeiger22 • 0
2
votes
1
reply
767
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
1
reply
698
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 12 months ago by • 0 • written 13 months ago by • 0
2
votes
1
reply
809
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
4
replies
1.2k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
14 months ago Philippine • 0
0
votes
2
replies
929
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 15 months ago by • 0
1
vote
1
reply
1.0k
views
WGCNA
DEGselection RNASeqData WGCNA
updated 15 months ago by ▴ 760 • written 15 months ago by • 0
1
vote
1
reply
744
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
vote
1
reply
920
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 16 months ago by 53k • written 16 months ago by • 0
1
vote
2
replies
3.5k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 16 months ago by • 0
1
vote
2
replies
781
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
16 months ago Gordon • 0
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 18 months ago by • 0
1
vote
3
replies
2.0k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
19 months ago Tanvi • 0
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 19 months ago by 68k • written 19 months ago by ▴ 50
0
votes
1
reply
691
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
1
reply
776
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 16 months ago by ▴ 20 • written 20 months ago by • 0
0
votes
1
reply
679
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
1
reply
707
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 21 months ago by 68k • written 21 months ago by • 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 22 months ago by 43k • written 23 months ago by ▴ 10
0
votes
0
replies
799
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
23 months ago Abril • 0
1
vote
2
replies
2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.7 years ago by • 0
1
vote
3
replies
1.3k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
24 months ago • updated 23 months ago island • 0
0
votes
2
replies
871
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
24 months ago Diana • 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
5
votes
6
replies
1.6k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
24 months ago Shaimaa Gamal • 0
1
vote
1
reply
1.0k
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
votes
2
replies
1.4k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
2.1 years ago Luca • 0
0
votes
1
reply
1.8k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
2
replies
1.3k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.1 years ago drewhaydensteele • 0
1
vote
1
reply
1.0k
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
vote
2
replies
2.0k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.1 years ago Levi • 0
0
votes
3
replies
2.8k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
2.1 years ago Oenone • 0
3
votes
4
replies
1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.2 years ago pl23 • 0
0
votes
1
reply
821
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 10
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.2 years ago Manthos • 0
0
votes
1
reply
937
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.2 years ago by ★ 13k • written 2.2 years ago by • 0
0
votes
2
replies
1.0k
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.2 years ago Ben ▴ 10
0
votes
2
replies
2.8k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
2.2 years ago RHEA • 0
2
votes
3
replies
2.8k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
152 results • Page 1 of 4
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Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
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Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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I updated the above answer today.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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