Showing : RNASeqData • reset
0
votes
1
reply
154
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 days ago by 50k • written 10 days ago by • 0
0
votes
1
reply
115
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 5 weeks ago by 65k • written 6 weeks ago by • 0
3
votes
5
replies
649
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 11 weeks ago by ▴ 10
0
votes
0
replies
232
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
12 weeks ago Abril • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
1
vote
3
replies
346
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
0
votes
2
replies
283
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
3 months ago Diana • 0
0
votes
1
reply
317
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
5
votes
6
replies
581
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
1
vote
1
reply
411
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
2
replies
360
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
0
votes
1
reply
352
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
1
vote
2
replies
459
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
1
vote
1
reply
342
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
vote
2
replies
684
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 0
0
votes
3
replies
719
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago Oenone • 0
3
votes
4
replies
545
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
0
votes
1
reply
355
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by 42k • written 5 months ago by ▴ 10
2
votes
2
replies
425
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
0
votes
1
reply
395
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 6 months ago by ★ 13k • written 6 months ago by • 0
0
votes
2
replies
448
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
6 months ago Ben • 0
0
votes
2
replies
718
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
6 months ago RHEA • 0
2
votes
3
replies
836
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
1
vote
1
reply
436
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
1
vote
7
replies
865
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
0
votes
1
reply
413
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
2
votes
4
replies
708
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
0
votes
4
replies
675
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
0
votes
1
reply
670
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
2
replies
525
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 0
1
vote
1
reply
468
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
0
replies
336
views
How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
8 months ago adi.rotem • 0
0
votes
1
reply
505
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 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
1
reply
513
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
2
votes
3
replies
1.1k
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 9 months ago by 65k • written 9 months ago by ▴ 10
0
votes
2
replies
1.0k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
2
replies
910
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
9 months ago Marina • 0
1
vote
2
replies
1.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 9 months ago by ▴ 120 • written 9 months ago by ▴ 10
0
votes
6
replies
791
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
2
replies
531
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 9 months ago by 42k • written 9 months ago by • 0
0
votes
0
replies
336
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
9 months ago sonal • 0
1
vote
9
replies
896
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
0
votes
0
replies
550
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
10 months ago info ▴ 10
0
votes
1
reply
518
views
DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
1
vote
1
reply
465
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 10 months ago by 50k • written 10 months ago by • 0
2
votes
1
reply
703
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
1
reply
573
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by ▴ 20
3
votes
3
replies
955
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
10 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue by shepherl 3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis by Guido Hooiveld ★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by zzrammal • 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Locations • All
France, 3 minutes ago
Spain, 5 minutes ago
United States, 5 minutes ago
Belgium, 6 minutes ago
France, 7 minutes ago
Traffic: 867 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6