Showing : RNASeqData • reset
22
votes
15
replies
7.5k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 6 months ago by ▴ 10 • written 2.1 years ago by ▴ 50
5
votes
6
replies
572
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
3
votes
3
replies
947
views
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 amnahsiddiqa ▴ 10
3
votes
4
replies
544
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
3
votes
2
replies
680
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
5
replies
644
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
2
votes
2
replies
416
views
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
2
votes
3
replies
1.1k
views
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 9 months ago by 65k • written 9 months ago by ▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 23 days ago by • 0 • written 11 months ago by • 0
2
votes
3
replies
1.2k
views
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 ★ 4.1k • written 10 months ago by ▴ 10
2
votes
3
replies
831
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
2
votes
4
replies
702
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
2
votes
1
reply
697
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
3
replies
341
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
1
reply
603
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
1
vote
2
replies
681
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 0
1
vote
1
reply
342
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
vote
1
reply
460
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
9
replies
891
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
1
vote
1
reply
430
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
1
vote
1
reply
410
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
2
replies
1.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 9 months ago by ▴ 120 • written 9 months ago by ▴ 10
1
vote
2
replies
452
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
1
vote
7
replies
855
views
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
1
vote
2
replies
528
views
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 42k • written 9 months ago by • 0
1
vote
1
reply
466
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
vote
1
reply
400
views
Deseq contrast question
RNASeqData DESeq2
updated 11 months ago by 42k • written 11 months ago by ▴ 10
0
votes
1
reply
111
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
votes
2
replies
715
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
6 months ago RHEA • 0
0
votes
1
reply
569
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by ▴ 20
0
votes
1
reply
350
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
1
reply
411
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
0
votes
1
reply
141
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 7 days ago by 50k • written 8 days ago by • 0
0
votes
1
reply
391
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 5 months ago by ★ 13k • written 6 months ago by • 0
0
votes
3
replies
714
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago Oenone • 0
0
votes
2
replies
355
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
0
votes
2
replies
1.0k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
0
replies
334
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
9 months ago sonal • 0
0
votes
4
replies
670
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 10
0
votes
0
replies
393
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
0
votes
6
replies
785
views
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
votes
1
reply
667
views
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
votes
1
reply
351
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by 42k • written 5 months ago by ▴ 10
0
votes
0
replies
230
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
12 weeks ago Abril • 0
0
votes
1
reply
504
views
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 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
0
replies
544
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
10 months ago info ▴ 10
0
votes
2
replies
930
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 23 days ago by • 0 • written 18 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Locations • All
France, 1 minute ago
United States, 5 minutes ago
United States, 7 minutes ago
United States, 47 minutes ago
EMBL Heidelberg, 1 hour ago
Traffic: 658 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6