Showing : RNASeqData • reset
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.0 years ago dantasezequiel1 • 0
2
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3
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1.4k
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RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 13 months ago by • 0 • written 13 months ago by • 0
0
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2
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656
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 14 months ago by ▴ 30 • written 14 months ago by • 0
1
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7
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844
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
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2
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1.1k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
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2
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2.6k
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Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 20 months ago by ★ 1.3k • written 20 months ago by • 0
3
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6
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1.3k
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Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
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10
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2.8k
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GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 9.9 years ago by ▴ 320 • written 9.9 years ago by ★ 6.8k
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1
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785
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
0
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6
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782
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
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1
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1.0k
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RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 80
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5
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2.2k
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
2.1 years ago • updated 23 months ago priyanka.m • 0
6
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4
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11k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.3 years ago by • 0 • written 3.2 years ago by ▴ 10
3
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4
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1.4k
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 years ago hgalmoore • 0
2
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4
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2.8k
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Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.5 years ago • updated 3.4 years ago ecg1g15 ▴ 20
0
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1
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657
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
0
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1
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564
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Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 20
1
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2
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1.6k
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Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 9.3 years ago by ★ 2.0k • written 9.3 years ago by ▴ 150
0
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2
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1.4k
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How to run vst transformation
RNASeqData vst
updated 24 months ago by 41k • written 2.0 years ago by • 0
0
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1
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643
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
2.1 years ago karl.stamm ▴ 10
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5
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1.4k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
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6
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1.4k
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.2 years ago Seaweed • 0
3
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2
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931
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
3.2 years ago Wuschel ▴ 10
0
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3
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704
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago Oenone • 0
22
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15
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7.5k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.1 years ago by ▴ 50
1
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1
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650
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 30
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3
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1.2k
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 2.2 years ago by ★ 1.3k • written 2.2 years ago by ▴ 10
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2
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347
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
0
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1
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559
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
1
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1
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598
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DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
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2
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1.2k
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lncRNA Genes in a Dataset
ncRNAtools RNASeqData
2.1 years ago sushimoto • 0
2
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8
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2.3k
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While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
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6
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1.2k
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while doing co-expression network analysis, I am getting an error
RNASeqData
3.1 years ago Rishav ▴ 20
2
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4
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1.2k
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
2.7 years ago khaveh ▴ 10
0
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3
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753
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 14 months ago by 50k • written 14 months ago by • 0
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523
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I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
1
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4
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1.0k
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
2.1 years ago sushimoto • 0
0
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4
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665
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
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5
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3.4k
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Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.4 years ago ecg1g15 ▴ 20
2
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9
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2.3k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
1
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4
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1.3k
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Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
16 months ago Iwan • 0
3
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3
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1.4k
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How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
23 months ago JK Kim ▴ 20
0
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1
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108
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 4 days ago by 50k • written 4 days ago by • 0
5
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6
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557
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
1
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1
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1.1k
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Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
1
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1
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335
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Differential gene expression analysis
RNASeqData RNAseq123
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
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2
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672
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Installation of R-packages for RNA-seq analysis
RNASeqData
14 months ago Begin-R • 0
0
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2
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631
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RNA-Seq and disease outcome analysis
rnaseqAnalysis RNASeqData
14 months ago JonasEnder • 0
8
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2
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6.9k
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
1
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1
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398
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Deseq contrast question
RNASeqData DESeq2
updated 10 months ago by 41k • written 11 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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