Showing : rnaseqdata • reset
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4
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559
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
28 days ago • updated 25 days ago Philippine • 0
0
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2
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317
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 4 weeks ago by • 0
3
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11
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699
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 weeks ago by • 0
1
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1
reply
279
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WGCNA
DEGselection RNASeqData WGCNA
updated 6 weeks ago by ▴ 760 • written 6 weeks ago by • 0
1
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1
reply
228
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
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1
reply
423
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Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 11 weeks ago by 51k • written 11 weeks ago by • 0
1
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2
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887
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 11 weeks ago by • 0
1
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2
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298
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
12 weeks ago Gordon • 0
0
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3
replies
552
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 4 months ago by ★ 4.5k • written 4 months ago by • 0
0
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4
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555
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 4 months ago by • 0
1
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3
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852
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
5 months ago Tanvi • 0
1
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3
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543
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 5 months ago by 67k • written 5 months ago by ▴ 50
0
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1
reply
346
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
0
votes
1
reply
352
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 11 weeks ago by ▴ 20 • written 6 months ago by • 0
0
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1
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377
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
1
reply
308
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 7 months ago by 67k • written 7 months ago by • 0
3
votes
5
replies
1.0k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 months ago by 42k • written 9 months ago by ▴ 10
0
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0
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492
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 months ago Abril • 0
1
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2
replies
1.7k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 18 months ago by • 0
1
vote
3
replies
659
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
9 months ago island • 0
0
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2
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497
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
10 months ago Diana • 0
0
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1
reply
706
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 10 months ago by ★ 4.5k • written 10 months ago by • 0
5
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6
replies
957
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
10 months ago Shaimaa Gamal • 0
1
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1
reply
628
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 11 months ago by ★ 4.5k • written 11 months ago by • 0
0
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2
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703
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
11 months ago Luca • 0
0
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1
reply
946
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 11 months ago by 67k • written 11 months ago by • 0
1
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2
replies
747
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
11 months ago drewhaydensteele • 0
1
vote
1
reply
615
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 11 months ago by ★ 4.5k • written 11 months ago by • 0
1
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2
replies
1.1k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
11 months ago Levi • 0
0
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3
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1.5k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
12 months ago Oenone • 0
3
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4
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924
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
12 months ago pl23 • 0
0
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1
reply
529
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 12 months ago by 42k • written 12 months ago by ▴ 10
2
votes
2
replies
673
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
12 months ago Manthos • 0
0
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1
reply
630
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 12 months ago by ★ 13k • written 12 months ago by • 0
0
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2
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673
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
12 months ago Ben ▴ 10
0
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2
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1.5k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
12 months ago RHEA • 0
2
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3
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1.6k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
1
vote
1
reply
695
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 13 months ago by 67k • written 13 months ago by • 0
1
vote
7
replies
1.2k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 11 months ago by 51k • written 13 months ago by • 0
0
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1
reply
662
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 13 months ago by ▴ 780 • written 14 months ago by • 0
2
votes
4
replies
1.1k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
14 months ago Shihui • 0
0
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4
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1.0k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 14 months ago by 67k • written 14 months ago by ▴ 10
3
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3
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2.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
14 months ago Ethan Nguyen • 0
1
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1
reply
1.1k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 14 months ago by 67k • written 14 months ago by • 0
0
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2
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783
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
14 months ago Beyza • 0
1
vote
1
reply
715
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
0
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0
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492
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
14 months ago adi.rotem • 0
0
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1
reply
673
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
0
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1
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774
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 15 months ago by ★ 4.5k • written 15 months ago by • 0
2
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3
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1.9k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 15 months ago by 67k • written 15 months ago by ▴ 10
50 results • Page 1 of 1
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Replies
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Votes
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
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