Showing : RNASeqData • reset
1
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.1 years ago demisa • 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
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 9.9 years ago by ★ 6.8k
1
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9
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886
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DESeq2 not replicable results
RNASeqData DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
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
2
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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 3.1 years ago by 50k • written 3.1 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 22 months ago by 65k • written 22 months ago by • 0
1
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7
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839
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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 6 months ago by • 0
3
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6
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8.8k
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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
5
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6
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554
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 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
0
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6
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779
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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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6
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1.2k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.1 years ago Rishav ▴ 20
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
0
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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
2.0 years ago • updated 23 months ago priyanka.m • 0
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 18 days ago by • 0 • written 10 months ago by • 0
7
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5
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3.4k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.4 years ago ecg1g15 ▴ 20
1
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5
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1.2k
views
Error in DEseq
DEseq RNASeqData
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
2
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5
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1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
3
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5
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626
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 10 weeks ago by ▴ 10
3
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4
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1.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 years ago hgalmoore • 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
0
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4
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1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
2
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4
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685
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
3
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4
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532
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 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
2
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4
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2.8k
views
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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4
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664
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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
1
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4
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1.0k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
2.1 years ago sushimoto • 0
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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703
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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
3
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3
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933
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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 amnahsiddiqa ▴ 10
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
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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 8 months ago by 65k • written 8 months ago by ▴ 10
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 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
2
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3
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1.4k
views
RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 13 months ago by • 0 • written 13 months ago by • 0
1
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3
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337
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
0
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3
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964
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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
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1.4k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
23 months ago JK Kim ▴ 20
1
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3
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1.7k
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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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1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
2.0 years ago Maka • 0
3
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3
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1.2k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
0
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3
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752
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 14 months ago by 50k • written 14 months ago by • 0
0
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3
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7.4k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
2
votes
3
replies
811
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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
0
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2
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346
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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823
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.2 years ago • updated 2.1 years ago m.glymenaki • 0
1
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2
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2.6k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 20 months ago by ★ 1.3k • written 20 months ago by • 0
1
vote
2
replies
1.6k
views
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
8
votes
2
replies
6.9k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
50 results • Page 1 of 1
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Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons by Michael Love 41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Votes
Print Differentially Expressed Exons From Dexseq Results
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
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