Showing : RNASeqData • reset
1
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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
1
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2
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1.1k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
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3
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704
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago Oenone • 0
22
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15
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7.5k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.1 years ago by ▴ 50
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2
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347
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
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1
reply
598
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DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
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1
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398
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Deseq contrast question
RNASeqData DESeq2
updated 10 months ago by 41k • written 11 months ago by ▴ 10
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3
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1.1k
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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
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1
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108
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 4 days ago by 50k • written 4 days ago by • 0
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2
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521
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago • updated 7 months ago Beyza • 0
0
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2
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882
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DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
9 months ago Marina • 0
0
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1
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590
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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 ★ 1.3k • written 11 months ago by • 0
0
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1
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512
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DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 10 months ago by 41k • written 10 months ago by • 0
0
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1
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111
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
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1
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425
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Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
2
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4
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689
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
0
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2
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692
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MA plot for DESEq2 analysis
RNASeqData DESeq2
6 months ago RHEA • 0
1
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3
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339
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
0
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1
reply
341
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
1
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2
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523
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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 41k • written 9 months ago by • 0
0
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4
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665
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
1
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1
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335
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Differential gene expression analysis
RNASeqData RNAseq123
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
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3
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1.1k
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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
5
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6
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557
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
2
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5
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1.4k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
0
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6
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782
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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
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1
reply
657
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
0
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1
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347
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by 41k • written 5 months ago by ▴ 10
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 days ago by • 0 • written 10 months ago by • 0
0
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1
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500
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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
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9
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887
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DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
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2
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921
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 19 days ago by • 0 • written 17 months ago by • 0
3
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3
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936
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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
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3
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814
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 6 months ago by ★ 1.3k • written 6 months ago by • 0
0
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1
reply
506
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Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 10 months ago by 41k • written 10 months ago by • 0
0
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2
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576
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RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 10 months ago by 50k • written 10 months ago by • 0
2
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2
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409
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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
5 months ago Manthos • 0
2
votes
1
reply
688
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
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1
reply
403
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
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1
reply
457
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
3
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5
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633
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 41k • written 10 weeks ago by ▴ 10
1
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2
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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
3
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4
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535
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
1
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2
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443
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
3
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2
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677
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
3
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3
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1.2k
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
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1
reply
508
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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
1
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1
reply
459
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
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4
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1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
12 months ago • updated 11 months ago ruba-mahmoud • 0
0
votes
1
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564
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Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 20
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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