Showing : rnaseqdata • reset
1
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15
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2.4k
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.0 years ago demisa • 0
22
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15
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7.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
0
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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 9.8 years ago by ▴ 320 • written 9.8 years ago by ★ 6.8k
2
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9
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2.2k
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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
vote
9
replies
852
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DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
2
votes
8
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2.3k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.0 years ago by 50k • written 3.0 years ago by ▴ 20
1
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7
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1.6k
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DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 21 months ago by 65k • written 21 months ago by • 0
1
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7
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796
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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
2
votes
6
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8.6k
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
2.1 years ago treebig44 ▴ 30
1
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6
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1.3k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.2 years ago Seaweed • 0
3
votes
6
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1.3k
views
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
5
votes
6
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515
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 weeks ago Shaimaa Gamal • 0
0
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6
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1.2k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.0 years ago Rishav ▴ 20
0
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6
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749
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 8 months ago by 50k • written 8 months ago by • 0
1
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5
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1.2k
views
Error in DEseq
DEseq RNASeqData
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
0
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5
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2.2k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
2.0 years ago • updated 23 months ago priyanka.m • 0
2
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5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 1 day ago by • 0 • written 10 months ago by • 0
7
votes
5
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3.3k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.4 years ago ecg1g15 ▴ 20
2
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5
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1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
3
votes
5
replies
585
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 7 weeks ago by ▴ 10
3
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4
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1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.0 years ago hgalmoore • 0
6
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4
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10k
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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 3.1 years ago by ▴ 10
2
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4
replies
1.2k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
2.6 years ago khaveh ▴ 10
2
votes
4
replies
642
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
6 months ago Shihui • 0
3
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4
replies
511
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
4 months ago pl23 • 0
2
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4
replies
2.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.4 years ago ecg1g15 ▴ 20
0
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4
replies
1.0k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
0
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4
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631
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 6 months ago by 65k • written 7 months ago by ▴ 10
1
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4
replies
1.0k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
2.1 years ago sushimoto • 0
1
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4
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1.2k
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Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
15 months ago Iwan • 0
1
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3
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315
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 weeks ago island • 0
4
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3
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1.2k
views
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
2
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3
replies
1.3k
views
RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 12 months ago by • 0 • written 12 months ago by • 0
0
votes
3
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659
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
4 months ago Oenone • 0
3
votes
3
replies
888
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
9 months ago amnahsiddiqa ▴ 10
0
votes
3
replies
945
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
3
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3
replies
1.1k
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
3
replies
1.3k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
22 months ago JK Kim ▴ 20
1
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3
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1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.0 years ago dantasezequiel1 • 0
0
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3
replies
725
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 14 months ago by 50k • written 14 months ago by • 0
2
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3
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1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
2
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3
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1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
23 months ago Maka • 0
0
votes
3
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7.3k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
2
votes
3
replies
756
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
2
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3
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1.0k
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 8 months ago by 65k • written 8 months ago by ▴ 10
0
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2
replies
870
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 1 day ago by • 0 • written 17 months ago by • 0
1
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2
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801
views
Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.1 years ago m.glymenaki • 0
0
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2
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316
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
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2
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2.5k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 19 months ago by ★ 1.3k • written 19 months ago by • 0
1
vote
2
replies
1.5k
views
Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 9.2 years ago by ★ 2.0k • written 9.2 years ago by ▴ 150
50 results • Page 1 of 1
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Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR by Gordon Smyth 50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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