Showing : RNASEQ • reset
0
votes
3
replies
151
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
2
replies
170
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 15 days ago by • 0
0
votes
2
replies
215
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
18 days ago • updated 15 days ago catv • 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 19 days ago by 42k • written 19 days ago by • 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
0
votes
1
reply
141
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 27 days ago by ★ 4.1k • written 29 days ago by • 0
0
votes
2
replies
235
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
2
votes
2
replies
266
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
0
votes
2
replies
278
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
1
vote
4
replies
309
views
DESeq2 Replicates
DESeq2 RNASeq
8 weeks ago kcarey • 0
1
vote
3
replies
369
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 weeks ago by ★ 1.3k • written 9 weeks ago by ▴ 10
0
votes
4
replies
304
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 weeks ago • updated 9 weeks ago mperalc • 0
0
votes
2
replies
304
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
votes
1
reply
267
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
3
votes
5
replies
635
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
3
votes
6
replies
539
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
11 weeks ago • updated 10 weeks ago boczniak767 ▴ 720
0
votes
0
replies
226
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 weeks ago Abril • 0
2
votes
2
replies
412
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
0
votes
4
replies
402
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
339
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
586
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
240
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 200 • written 3 months ago by • 0
2
votes
4
replies
599
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
4
votes
6
replies
606
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
1
reply
304
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
3
replies
496
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
votes
1
reply
272
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
1
vote
2
replies
470
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
2
votes
3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
1
vote
2
replies
445
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
replies
812
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
1
reply
378
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 42k • written 5 months ago by • 0
2
votes
3
replies
480
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
0
votes
3
replies
460
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
2
votes
2
replies
410
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
4
replies
612
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
1
vote
4
replies
637
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
0
votes
0
replies
360
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
4
votes
2
replies
640
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
0
votes
6
replies
867
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
votes
2
replies
542
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 6 months ago by ★ 1.0k • written 6 months ago by ▴ 190
0
votes
1
reply
445
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
0
votes
0
replies
339
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
0
votes
2
replies
644
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
0
votes
0
replies
286
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
0
votes
0
replies
342
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
0
votes
0
replies
357
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
6 months ago Sara • 0
1
vote
1
reply
426
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
1
vote
7
replies
847
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Awards • All
Popular Question to Gyan Prakash Mishra ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Locations • All
United States, 4 minutes ago
India, 24 minutes ago
Canada, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 418 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