Showing : RnaSeq • reset
3
votes
2
replies
1.1k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
15 months ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
584
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
16 months ago Bibi • 0
10
votes
11
replies
3.0k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 15 months ago by • 0 • written 8.1 years ago by ▴ 80
1
vote
3
replies
996
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 16 months ago by 53k • written 16 months ago by • 0
0
votes
3
replies
1.3k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
0
votes
1
reply
793
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
2
replies
722
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 16 months ago by • 0
0
votes
2
replies
1.1k
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
17 months ago • updated 16 months ago catv • 0
5
votes
3
replies
1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 16 months ago by 53k • written 17 months ago by • 0
0
votes
1
reply
1.2k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
1
reply
888
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
0
votes
2
replies
1.9k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
18 months ago • updated 17 months ago kcarey • 0
2
votes
2
replies
748
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
18 months ago Sabiha ▴ 20
0
votes
2
replies
3.0k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
18 months ago kcarey • 0
1
vote
4
replies
838
views
DESeq2 Replicates
DESeq2 RNASeq
18 months ago kcarey • 0
1
vote
3
replies
979
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 18 months ago by ★ 1.4k • written 18 months ago by ▴ 10
0
votes
4
replies
948
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
18 months ago mperalc • 0
0
votes
2
replies
1.1k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 18 months ago by 53k • written 18 months ago by • 0
3
votes
5
replies
1.6k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 18 months ago by 43k • written 18 months ago by ▴ 10
2
votes
1
reply
687
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 18 months ago by 43k • written 18 months ago by ▴ 10
3
votes
7
replies
1.8k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
19 months ago • updated 17 hours ago boczniak767 ▴ 740
0
votes
0
replies
719
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
19 months ago Abril • 0
2
votes
2
replies
1.6k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
19 months ago jackafiore • 0
1
vote
2
replies
2.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.4 years ago by • 0
0
votes
4
replies
945
views
Ballgown error in scan for c.tab files
ballgown RNASeq
19 months ago candacenewcome • 0
1
vote
3
replies
1.1k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
19 months ago island • 0
1
vote
3
replies
1.2k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 19 months ago by • 0
0
votes
1
reply
608
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 19 months ago by ▴ 220 • written 19 months ago by • 0
2
votes
4
replies
2.0k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
20 months ago • updated 19 months ago Sabiha ▴ 20
4
votes
6
replies
1.5k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 19 months ago by 53k • written 20 months ago by • 0
3
votes
1
reply
790
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
3
replies
1.5k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 20 months ago by • 0
0
votes
1
reply
721
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
20 months ago WS • 0
2
votes
3
replies
3.4k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 20 months ago by ★ 1.4k • written 21 months ago by • 0
1
vote
2
replies
1.2k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
21 months ago Sabiha ▴ 20
1
vote
2
replies
1.1k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
21 months ago drewhaydensteele • 0
12
votes
5
replies
4.8k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 3 months ago by • 0 • written 21 months ago by • 0
0
votes
3
replies
1.2k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
21 months ago Karthik • 0
1
vote
1
reply
712
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
2
votes
3
replies
1.4k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
21 months ago Karthik • 0
2
votes
2
replies
983
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
22 months ago Manthos • 0
2
votes
4
replies
1.3k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
22 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
764
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 22 months ago by 43k • written 23 months ago by • 0
0
votes
2
replies
1.2k
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 22 months ago by ★ 1.1k • written 22 months ago by ▴ 200
0
votes
9
replies
3.1k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 22 months ago by • 0 • written 7.9 years ago by ▴ 60
1
vote
4
replies
1.4k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
22 months ago Wending • 0
0
votes
0
replies
787
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
22 months ago mch • 0
5
votes
2
replies
2.1k
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 22 months ago by 53k • written 22 months ago by ▴ 10
0
votes
6
replies
2.2k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
22 months ago erika.maldonado-rosado • 0
0
votes
0
replies
706
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
23 months ago Sara • 0
1,407 results • Page 2 of 29
Recent ...
Replies
Answer: DESeq2 used with zinbwave weights - Differences on contrasts calculations by eja.gsee.r.m • 0
Hi your issue with DESeq2 contrasts and zinbwave weights sounds like it might stem from how weights are integrated during the different con…
Comment: How to analyze Affy data, CEL files not available by eja.gsee.r.m • 0
When analyzing data without raw files like Bobby MAS expression measures t important to work within the limits of the available informatio…
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Awards • All
Popular Question to Assa Yeroslaviz ★ 1.5k
Popular Question to Nik dAK ▴ 10
Popular Question to Michael • 0
Popular Question to sum31278 • 0
Popular Question to Gordon Smyth 53k
Locations • All
Pittsburgh, United States, 13 minutes ago
Singapore, 31 minutes ago
WEHI, Melbourne, Australia, 2 hours ago
Pakistan, 3 hours ago
The city by the bay, 6 hours ago
Traffic: 768 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