Showing : RNASeqData • 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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3
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241
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
updated 16 days ago by 51k • written 16 days ago by • 0
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3
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331
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
5 weeks ago Tanvi • 0
1
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3
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332
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 weeks ago by 66k • written 6 weeks ago by ▴ 50
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1
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198
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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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147
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
10 weeks ago Shaimaa Gamal • 0
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1
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254
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 weeks ago by 51k • written 12 weeks ago by • 0
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1
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196
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 3 months ago by 66k • written 3 months ago by • 0
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5
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808
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 4 months ago by 42k • written 5 months ago by ▴ 10
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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
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2
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1.4k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 14 months ago by • 0
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3
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481
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
5 months ago island • 0
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2
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373
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
6 months ago Diana • 0
0
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1
reply
491
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 6 months ago by ★ 4.2k • written 6 months ago by • 0
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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
1
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1
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482
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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
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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
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1
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534
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 7 months ago by 66k • written 7 months ago by • 0
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2
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587
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
7 months ago drewhaydensteele • 0
1
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1
reply
431
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Differential gene expression analysis
RNASeqData RNAseq123
updated 7 months ago by ★ 4.2k • written 8 months ago by • 0
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2
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857
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
8 months ago • updated 7 months ago Levi • 0
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3
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909
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
8 months ago Oenone • 0
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4
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675
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
8 months ago pl23 • 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
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2
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530
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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
8 months ago Manthos • 0
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1
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500
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 8 months ago by ★ 13k • written 8 months ago by • 0
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2
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531
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
8 months ago Ben • 0
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984
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MA plot for DESEq2 analysis
RNASeqData DESeq2
8 months ago RHEA • 0
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3
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1.1k
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 9 months ago by ★ 1.4k • written 9 months ago by • 0
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1
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526
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Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 9 months ago by 66k • written 9 months ago by • 0
1
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7
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1.0k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 7 months ago by 51k • written 9 months ago by • 0
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1
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494
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 9 months ago by ▴ 780 • written 10 months ago by • 0
2
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4
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881
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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
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4
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814
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 10 months ago by 66k • written 10 months ago by ▴ 10
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3
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1.6k
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
10 months ago Ethan Nguyen • 0
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1
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798
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 10 months ago by 66k • 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
1
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1
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566
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bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
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0
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391
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How to use erccdashboard with erccmix="Single" design
RNASeqData erccdashboard
10 months ago adi.rotem • 0
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1
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566
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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 11 months ago by ★ 4.2k • written 11 months ago by • 0
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615
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Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData DEGseq
updated 11 months ago by ★ 4.2k • written 11 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 11 months ago by 66k • written 11 months ago by ▴ 10
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2
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1.3k
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 11 months ago by 66k • written 11 months ago by • 0
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2
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1.2k
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DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
12 months ago • updated 11 months ago Marina • 0
1
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2
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1.8k
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IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 12 months ago by ▴ 120 • written 12 months ago by ▴ 10
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6
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899
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 12 months ago by 51k • written 12 months ago by • 0
1
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2
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625
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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 12 months ago by 42k • written 12 months ago by • 0
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0
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412
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
12 months ago sonal • 0
1
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9
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1.0k
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DESeq2 not replicable results
RNASeqData DESeq2
updated 12 months ago by 42k • written 12 months ago by • 0
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0
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637
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
12 months ago info ▴ 10
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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