Showing : DifferentialExpression • reset
0
votes
1
reply
549
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 6 months ago by • 0
1
vote
1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
1
vote
8
replies
2.9k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
7 months ago ktz • 0
0
votes
3
replies
962
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
387
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
1
reply
601
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
5
replies
693
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 months ago by • 0
0
votes
2
replies
696
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
11 months ago Tadeoye ▴ 20
0
votes
9
replies
1.7k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 11 months ago by 68k • written 11 months ago by • 0
3
votes
3
replies
905
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 11 months ago by 53k • written 11 months ago by • 0
1
vote
3
replies
856
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
12 months ago • updated 11 months ago abadgerw • 0
0
votes
5
replies
1.2k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
12 months ago • updated 11 months ago abadgerw • 0
0
votes
1
reply
515
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
6
replies
1.4k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 12 months ago by 43k • written 13 months ago by • 0
0
votes
3
replies
947
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 14 months ago by 53k • written 14 months ago by • 0
3
votes
3
replies
1.6k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
3
replies
1.0k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 15 months ago by • 0
3
votes
5
replies
2.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
0
votes
3
replies
974
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
2
votes
5
replies
1.1k
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 15 months ago by 68k • written 16 months ago by • 0
0
votes
0
replies
783
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
16 months ago nhaus ▴ 70
3
votes
5
replies
3.3k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 16 months ago by • 0 • written 20 months ago by ▴ 60
2
votes
1
reply
805
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by ▴ 70
0
votes
4
replies
1.2k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
17 months ago vohara4 • 0
0
votes
1
reply
633
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
3
replies
772
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 18 months ago by • 0
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
1
reply
618
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
2
votes
7
replies
1.9k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
18 months ago sajadahmad41454 • 0
0
votes
3
replies
1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
votes
3
replies
895
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
2
replies
809
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by ▴ 70
5
votes
6
replies
1.5k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by ▴ 70
1
vote
3
replies
894
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
2
replies
994
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
2
replies
866
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
20 months ago • updated 19 months ago Chanderkant Chaudhary • 0
8
votes
5
replies
3.2k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 months ago by 53k • written 20 months ago by ▴ 60
0
votes
2
replies
854
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
2
replies
1.2k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
1
vote
3
replies
1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 21 months ago by • 0
0
votes
4
replies
1.0k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
20 months ago mperalc • 0
0
votes
0
replies
756
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
21 months ago Abril • 0
2
votes
1
reply
782
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
3
votes
2
replies
1.0k
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
21 months ago Shaimaa Gamal • 0
4
votes
3
replies
1.1k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 21 months ago by 53k • written 21 months ago by • 0
2
votes
3
replies
1.1k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 21 months ago by 68k • written 21 months ago by • 0
2
votes
1
reply
741
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by ▴ 20
0
votes
2
replies
831
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
5
votes
6
replies
1.5k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
22 months ago • updated 21 months ago Shaimaa Gamal • 0
4
votes
6
replies
1.6k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 21 months ago by 53k • written 22 months ago by • 0
198 results • Page 1 of 4
Recent ...
Replies
Comment: After running samtools, the featureCounts command crashed. by surprised.swordtail.tlfy • 0
Hey Rui, that's a tricky error! Kevin's suggestion about the GTF file makes total sense. I've had similar issues with file paths in WSL cau…
Comment: How to reverse complement some elements of a DNAStringSet by Lenson • 0
Hey, thanks for the insightful post! I totally get what you mean about the learning process. Sometimes you try a new approach and it just d…
Comment: Research and Service Group Leader positions in AI in Biology at EMBL by eja.gssssswssswwse.r.m • 0
For mobile gamers seeking innovative experiences, free download ck999 game brings engaging gameplay right to your device. Whether exploring…
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
Locations • All
United States, 30 minutes ago
Australia, 31 minutes ago
United States, 1 hour ago
Brazil, 1 hour ago
Germany, 2 hours ago
Traffic: 879 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