Showing : differentialexpression • reset
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
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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413
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 weeks ago • updated 19 days ago abadgerw • 0
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608
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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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1
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186
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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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827
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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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3
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551
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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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3
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521
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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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5
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1.0k
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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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582
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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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636
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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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1
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448
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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
0
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1
reply
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
1
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3
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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
2
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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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796
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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
0
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2
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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
1
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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
0
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2
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474
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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 6 weeks ago by 52k • written 9 months ago by ▴ 50
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2
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578
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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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2
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693
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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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676
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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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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
reply
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
3
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2
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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
reply
453
views
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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990
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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
reply
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
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
0
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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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874
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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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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…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Thanks for this. If your data is from 450K, you'll have to call your DMRs in hg19, and then lift the DMR ranges over to hg38 p…
Votes
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)
Answer: Deseq2 Design
Answer: Fold change calculation in Diffbind vs. DESEQ2?
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