Showing : RNASeqData • reset
22
votes
15
replies
7.5k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 6 months ago by ▴ 10 • written 2.1 years ago by ▴ 50
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
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
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
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
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
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 25 days ago by • 0 • written 11 months ago by • 0
0
votes
4
replies
1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
12 months ago ruba-mahmoud • 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
3
votes
3
replies
950
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
0
votes
2
replies
933
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 24 days ago by • 0 • written 18 months ago by • 0
0
votes
2
replies
904
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
9 months ago Marina • 0
1
vote
9
replies
892
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
1
vote
7
replies
863
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
2
votes
3
replies
835
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
0
votes
6
replies
789
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
0
votes
3
replies
717
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago Oenone • 0
0
votes
2
replies
716
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
6 months ago RHEA • 0
2
votes
4
replies
705
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
2
votes
1
reply
701
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
1
vote
2
replies
683
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 0
3
votes
2
replies
682
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
0
votes
4
replies
671
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
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
3
votes
5
replies
647
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 11 weeks ago by ▴ 10
1
vote
1
reply
606
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
1
reply
601
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
5
votes
6
replies
580
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
0
votes
2
replies
578
views
RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 10 months ago by 50k • written 10 months ago by • 0
0
votes
1
reply
571
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by ▴ 20
0
votes
0
replies
547
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
10 months ago info ▴ 10
3
votes
4
replies
544
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
1
vote
2
replies
529
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
2
replies
525
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 0
0
votes
1
reply
516
views
DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
0
votes
1
reply
513
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 10 months ago by 42k • written 11 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 8 months ago by ★ 4.1k • written 8 months ago by • 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
1
vote
1
reply
467
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
1
reply
466
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
1
reply
464
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
1
vote
2
replies
458
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 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
1
vote
1
reply
434
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
2
votes
2
replies
424
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
412
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 7 months ago by ▴ 780 • written 7 months ago by • 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
1
vote
1
reply
400
views
Deseq contrast question
RNASeqData DESeq2
updated 11 months ago by 42k • written 11 months ago by ▴ 10
0
votes
1
reply
394
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 5 months ago by ★ 13k • written 6 months ago by • 0
50 results • Page 1 of 1
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Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
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