Showing : rnaseqdata • reset
22
votes
15
replies
7.3k
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
1
vote
9
replies
851
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
1
vote
7
replies
792
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
0
votes
6
replies
748
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 8 months ago by 50k • written 8 months ago by • 0
5
votes
6
replies
514
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 weeks ago Shaimaa Gamal • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 1 day ago by • 0 • written 10 months ago by • 0
3
votes
5
replies
583
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 7 weeks ago by ▴ 10
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
0
votes
4
replies
628
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 6 months ago by 65k • written 6 months ago by ▴ 10
2
votes
4
replies
641
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
6 months ago Shihui • 0
3
votes
4
replies
510
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
4 months ago pl23 • 0
0
votes
4
replies
1.0k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
2
votes
3
replies
755
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 5 months ago by ★ 1.3k • written 5 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 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
3
votes
3
replies
884
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
9 months ago amnahsiddiqa ▴ 10
0
votes
3
replies
656
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
4 months ago Oenone • 0
1
vote
3
replies
312
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 weeks ago island • 0
2
votes
3
replies
1.0k
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
3
votes
3
replies
1.1k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
1
vote
2
replies
636
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago • updated 3 months ago Levi • 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
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 8 months ago by ▴ 120 • written 8 months ago by ▴ 10
1
vote
2
replies
411
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
3
votes
2
replies
655
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 9 months ago by 50k • written 9 months ago by ▴ 10
0
votes
2
replies
610
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
5 months ago RHEA • 0
0
votes
2
replies
419
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
5 months ago Ben • 0
0
votes
2
replies
242
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
11 weeks ago Diana • 0
0
votes
2
replies
485
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
0
votes
2
replies
981
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
2
replies
811
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
8 months ago Marina • 0
0
votes
2
replies
865
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 23 hours ago by • 0 • written 17 months ago by • 0
0
votes
2
replies
552
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
383
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
4 months ago Manthos • 0
1
vote
2
replies
500
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 8 months ago by 41k • written 9 months ago by • 0
0
votes
2
replies
316
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
0
votes
1
reply
317
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
0
votes
1
reply
384
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 6 months ago by ▴ 770 • written 6 months ago by • 0
0
votes
1
reply
353
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 5 months ago by ★ 13k • written 5 months ago by • 0
1
vote
1
reply
568
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
1
vote
1
reply
390
views
Deseq contrast question
RNASeqData DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 10
1
vote
1
reply
308
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
votes
1
reply
623
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
318
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by 41k • written 5 months ago by ▴ 10
0
votes
1
reply
487
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
0
votes
1
reply
488
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
2
votes
1
reply
652
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
0
votes
1
reply
256
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 12 weeks ago by ★ 4.0k • written 12 weeks ago by • 0
1
vote
1
reply
377
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
1
vote
1
reply
440
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
0
votes
1
reply
486
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
50 results • Page 1 of 1
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Replies
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Answer: rlog transformation by Michael Love 41k
It is dependent on the other samples in the dataset.
Answer: ONT long-read RNA sequencing - data analysis options by Michael Love 41k
*"This worked really well for brain but has not work as well for lung as I get #N/A for many padj"* See the vignette for the cause of th…
Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by Michael Love 41k
Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matr…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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