Showing : rnaseqdata • reset
1
vote
7
replies
815
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
22
votes
15
replies
7.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
0
votes
2
replies
327
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
vote
1
reply
580
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
1
vote
1
reply
392
views
Deseq contrast question
RNASeqData DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 10
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 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
3
replies
678
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago • updated 4 months ago Oenone • 0
0
votes
2
replies
506
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
0
votes
2
replies
842
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
8 months ago Marina • 0
0
votes
1
reply
578
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 ★ 1.3k • written 11 months ago by • 0
0
votes
1
reply
494
views
DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
votes
1
reply
98
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 24 days ago by 65k • written 25 days ago by • 0
1
vote
1
reply
404
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
2
votes
4
replies
658
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
0
votes
2
replies
640
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
5 months ago RHEA • 0
1
vote
3
replies
322
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
12 weeks ago island • 0
0
votes
1
reply
325
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
1
vote
2
replies
508
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 41k • written 9 months ago by • 0
0
votes
4
replies
650
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
1
vote
1
reply
322
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
2
votes
3
replies
1.1k
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 ★ 4.0k • written 10 months ago by ▴ 10
5
votes
6
replies
529
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
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
0
votes
6
replies
760
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
1
reply
641
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
votes
1
reply
330
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 41k • written 5 months ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 days ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
493
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 7 months ago by ★ 4.0k • written 7 months ago by • 0
1
vote
9
replies
869
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
votes
2
replies
890
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 days ago by • 0 • written 17 months ago by • 0
3
votes
3
replies
914
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
769
views
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
votes
1
reply
497
views
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
votes
2
replies
562
views
RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 10 months ago by 50k • written 10 months ago by • 0
2
votes
2
replies
392
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
2
votes
1
reply
666
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 9 months ago by 65k • written 9 months ago by • 0
1
vote
1
reply
390
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
1
vote
1
reply
447
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
5
replies
605
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
1
vote
2
replies
1.4k
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
votes
4
replies
520
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
423
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
3
votes
2
replies
665
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
votes
3
replies
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
votes
1
reply
494
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
1
vote
1
reply
442
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
votes
4
replies
1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
0
votes
1
reply
549
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by ▴ 20
0
votes
2
replies
427
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
5 months ago Ben • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Awards • All
Popular Question to James W. MacDonald 65k
Scholar to Michael Love 41k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Locations • All
France, 3 minutes ago
United States, 15 minutes ago
Sweden, 18 minutes ago
United States, 19 minutes ago
The Netherlands, 27 minutes ago
Traffic: 1119 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