Showing : DifferentialExpression • reset
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
8 days ago • updated 7 days ago Tadeoye ▴ 20
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9
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 12 days ago by 67k • written 18 days ago by • 0
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528
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 27 days ago by 52k • written 27 days ago by • 0
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 weeks ago • updated 20 days ago abadgerw • 0
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 weeks ago • updated 15 days ago abadgerw • 0
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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6
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828
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 7 weeks ago by 43k • written 10 weeks ago by • 0
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 3 months ago by 52k • written 3 months ago by • 0
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3
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735
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 4 months ago by 67k • written 4 months ago by • 0
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 4 months ago by • 0
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
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3
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 4 months ago by ★ 4.6k • written 4 months ago by • 0
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5
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 4 months ago by 67k • written 5 months ago by • 0
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414
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
5 months ago nhaus ▴ 70
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5
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1.7k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 months ago by • 0 • written 9 months ago by ▴ 50
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by ▴ 70
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4
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619
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 months ago vohara4 • 0
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1
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365
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by • 0
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3
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422
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 months ago by 43k • written 7 months ago by • 0
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654
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 months ago by 52k • written 7 months ago by • 0
0
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1
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390
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
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7
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1.1k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
7 months ago sajadahmad41454 • 0
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3
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
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3
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544
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
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516
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 8 months ago by 43k • written 8 months ago by ▴ 70
5
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6
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880
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 8 months ago by ★ 4.6k • written 8 months ago by ▴ 70
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3
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555
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
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2
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475
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
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2
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509
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
9 months ago • updated 8 months ago Chanderkant Chaudhary • 0
6
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5
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1.8k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 52k • written 9 months ago by ▴ 50
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 months ago by 52k • written 9 months ago by • 0
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694
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 9 months ago by 43k • written 9 months ago by • 0
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3
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734
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 10 months ago by • 0
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4
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677
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 months ago mperalc • 0
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512
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 months ago Abril • 0
2
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1
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527
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
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596
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 months ago Shaimaa Gamal • 0
4
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3
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734
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
2
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3
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686
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 months ago by 67k • written 10 months ago by • 0
2
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1
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453
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by ▴ 20
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2
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555
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by • 0
5
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6
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991
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
11 months ago Shaimaa Gamal • 0
4
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6
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1.1k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 months ago by 52k • written 11 months ago by • 0
3
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1
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602
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 11 months ago by 52k • written 11 months ago by • 0
1
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3
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917
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 12 months ago by • 0
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5
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1.0k
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Help with model for differential expression analysis
DifferentialExpression edgeR
11 months ago • updated 10 months ago Lucy ▴ 60
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3
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723
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
1
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1
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651
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
2
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4
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875
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 11 months ago by 52k • written 12 months ago by • 0
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2
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738
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
12 months ago Luca • 0
50 results • Page 1 of 1
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Replies
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10
Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…
Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k
I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…
Votes
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
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