Showing : DifferentialExpression • reset
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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 3 days ago by ★ 4.2k • written 3 days ago by • 0
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5
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 3 days ago by 66k • written 9 days ago by • 0
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
17 days ago nhaus ▴ 50
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948
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 4 weeks ago by • 0 • written 4 months ago by ▴ 50
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233
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by ▴ 50
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339
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 weeks ago vohara4 • 0
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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 7 weeks ago by 66k • written 7 weeks ago by • 0
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3
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260
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
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3
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402
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 weeks ago by 51k • written 10 weeks ago by • 0
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264
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 weeks ago by ★ 4.2k • written 11 weeks ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
11 weeks ago • updated 10 weeks ago sajadahmad41454 • 0
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414
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 12 weeks ago by ★ 4.2k • written 12 weeks ago by • 0
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3
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370
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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 12 weeks ago by 66k • written 12 weeks ago by • 0
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2
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340
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by ▴ 50
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6
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619
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 3 months ago by ★ 4.2k • written 3 months ago by ▴ 50
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3
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375
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 3 months ago by 66k • written 3 months ago by • 0
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2
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264
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 3 months ago by 66k • written 3 months ago by • 0
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2
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345
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 months ago Chanderkant Chaudhary • 0
5
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3
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941
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 4 months ago by 51k • written 4 months ago by ▴ 50
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2
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388
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 4 months ago by 51k • written 4 months ago by • 0
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448
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 4 months ago by 42k • written 4 months ago by • 0
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3
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546
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 5 months ago by • 0
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4
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463
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
5 months ago • updated 4 months ago mperalc • 0
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362
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
5 months ago Abril • 0
2
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1
reply
391
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 5 months ago by ★ 4.2k • written 5 months ago by • 0
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2
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422
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
5 months ago Shaimaa Gamal • 0
4
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3
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507
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 5 months ago by 51k • written 5 months ago by • 0
2
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3
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479
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 5 months ago by 66k • written 5 months ago by • 0
2
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1
reply
300
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 5 months ago by 42k • written 5 months ago by ▴ 20
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2
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415
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 5 months ago by 42k • written 5 months ago by • 0
5
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6
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722
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
6 months ago Shaimaa Gamal • 0
4
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6
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797
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 5 months ago by 51k • written 6 months ago by • 0
3
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1
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429
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 6 months ago by 51k • written 6 months ago by • 0
1
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3
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704
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 7 months ago by • 0
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5
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786
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Help with model for differential expression analysis
DifferentialExpression edgeR
6 months ago Lucy ▴ 60
0
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3
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518
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 7 months ago by ★ 4.2k • written 7 months ago by • 0
1
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1
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482
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 7 months ago by ★ 4.2k • written 7 months ago by • 0
2
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4
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670
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 6 months ago by 51k • written 7 months ago by • 0
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2
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479
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
7 months ago Luca • 0
1
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2
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648
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 7 months ago by 51k • written 7 months ago by • 0
0
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1
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439
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 8 months ago by 42k • written 8 months ago by ▴ 10
1
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4
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682
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 8 months ago by 42k • written 8 months ago by ▴ 60
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8
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940
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
8 months ago Luca • 0
0
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0
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471
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
9 months ago nromerov • 0
2
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6
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904
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 9 months ago by 16k • written 9 months ago by • 0
2
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4
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880
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
10 months ago Shihui • 0
0
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1
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515
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''Model_Matrix'' error
DifferentialExpression limma
updated 10 months ago by 51k • written 10 months ago by • 0
3
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3
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661
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 10 months ago by 66k • written 10 months ago by • 0
0
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3
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547
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
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2
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636
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
10 months ago Beyza • 0
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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