Showing : rnaseqdata • reset
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 23 days ago by 65k • written 24 days ago by • 0
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 weeks ago Abril • 0
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
12 weeks ago island • 0
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255
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
12 weeks ago Diana • 0
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271
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
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388
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
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323
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
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324
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
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1
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320
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Differential gene expression analysis
RNASeqData RNAseq123
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
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651
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago Levi • 0
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
4 months ago Oenone • 0
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
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326
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by 41k • written 5 months ago by ▴ 10
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
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361
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 5 months ago by ★ 13k • written 5 months ago by • 0
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425
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
5 months ago Ben • 0
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636
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MA plot for DESEq2 analysis
RNASeqData DESeq2
5 months ago RHEA • 0
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3
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 6 months ago by ★ 1.3k • written 6 months ago by • 0
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403
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Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
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7
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813
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
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389
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 6 months ago by ▴ 780 • written 6 months ago by • 0
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4
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655
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago • updated 6 months ago Shihui • 0
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4
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648
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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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1.2k
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
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639
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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
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501
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
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440
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bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
7 months ago adi.rotem • 0
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491
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
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492
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Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
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bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
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997
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
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DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
8 months ago Marina • 0
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1.4k
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IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 8 months ago by ▴ 120 • written 9 months ago by ▴ 10
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758
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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
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507
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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
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322
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
9 months ago sonal • 0
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865
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DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
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522
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
9 months ago info ▴ 10
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486
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DESeq2, Timecourse using fitted splines
timecoursedata RNASeqData TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
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444
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
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663
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Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 9 months ago by 65k • written 9 months ago by • 0
0
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1
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546
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Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by ▴ 20
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909
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how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
10 months ago • updated 9 months ago amnahsiddiqa ▴ 10
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1.1k
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PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
50 results • Page 1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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