Showing : RNASeqData • reset
22
votes
15
replies
7.6k
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
9
replies
906
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
1
vote
7
replies
873
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
5
votes
6
replies
596
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
0
votes
6
replies
805
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
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
5
replies
664
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 11 weeks ago by ▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 29 days ago by • 0 • written 11 months ago by • 0
3
votes
4
replies
556
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
4
replies
688
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
2
votes
4
replies
721
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
3
votes
3
replies
970
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
851
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
3
replies
731
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago Oenone • 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
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
8 months ago Ethan Nguyen • 0
1
vote
3
replies
357
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 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
2
votes
2
replies
436
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
1
vote
2
replies
539
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 10 months ago by • 0
1
vote
2
replies
697
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 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
2
replies
1.6k
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
1
vote
2
replies
468
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
3
votes
2
replies
687
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
2
replies
467
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
289
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
3 months ago Diana • 0
0
votes
2
replies
372
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
0
votes
2
replies
939
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
9 months ago Marina • 0
0
votes
2
replies
534
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 0
0
votes
2
replies
949
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 29 days ago by • 0 • written 18 months ago by • 0
0
votes
2
replies
1.1k
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
583
views
RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
2
replies
743
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
6 months ago RHEA • 0
0
votes
1
reply
360
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
1
reply
418
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 14 days ago by 50k • written 14 days ago by • 0
0
votes
1
reply
404
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
1
vote
1
reply
611
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
1
vote
1
reply
401
views
Deseq contrast question
RNASeqData DESeq2
updated 11 months ago by 42k • written 11 months ago by ▴ 10
1
vote
1
reply
352
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
0
votes
1
reply
681
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
1
reply
365
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 6 months ago by ▴ 10
0
votes
1
reply
510
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
515
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 11 months ago by 42k • written 11 months ago by • 0
2
votes
1
reply
715
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
328
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
vote
1
reply
415
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
469
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
0
votes
1
reply
530
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
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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