Showing : deg • reset
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586
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
12 months ago Abril • 0
5
votes
2
replies
1.2k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 15 months ago by 52k • written 15 months ago by • 0
0
votes
1
reply
941
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 16 months ago by • 0 • written 3.6 years ago by • 0
3
votes
11
replies
1.9k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 20 months ago by 52k • written 20 months ago by • 0
0
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1
reply
874
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 23 months ago by 52k • written 23 months ago by • 0
0
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5
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2.7k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
2.5 years ago • updated 2.3 years ago marinaw ▴ 20
0
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6
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1.9k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
2.6 years ago Weiqian ▴ 10
1
vote
7
replies
2.4k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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0
replies
1.0k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.8 years ago zroger499 • 0
0
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5
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6.3k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 2.5 years ago by • 0 • written 3.0 years ago by • 0
0
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6
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4.7k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 60
2
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4
replies
2.7k
views
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma toptable deg logfc
written 6.5 years ago by • 0
2
votes
6
replies
5.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.7 years ago reganhayward • 0
3
votes
3
replies
2.8k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
1
vote
3
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1.1k
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
4
votes
5
replies
1.8k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 5.1 years ago by 52k • written 5.1 years ago by ▴ 40
0
votes
2
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914
views
same results changing contrast function
deseq2 contrast DEG
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
4
replies
1.5k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 5.4 years ago by ★ 13k • written 5.4 years ago by • 0
2
votes
6
replies
1.9k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
1
vote
2
replies
2.1k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 5.4 years ago by 52k • written 5.4 years ago by • 0
0
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0
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1.1k
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DEG among experimental and control group in MAST
MAST DEG batch effects
5.4 years ago chendianyu • 0
0
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2
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1.0k
views
different designs for finding DEG by limma
limma DEG design
5.5 years ago amin.ghareyazi • 0
1
vote
1
reply
973
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 30
5
votes
13
replies
3.4k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
8
replies
1.5k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
7
replies
2.3k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
6.9 years ago • updated 6.0 years ago SPbeginner • 0
1
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5
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2.1k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
3
votes
4
replies
2.2k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 30
0
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0
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1.6k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.8 years ago vharshavardhanan • 0
0
votes
3
replies
2.2k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
6
votes
14
replies
3.5k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 6.9 years ago by ▴ 840 • written 6.9 years ago by ▴ 30
1
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0
replies
2.5k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.0 years ago digrigor ▴ 10
0
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0
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1.9k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
7.0 years ago lawarde.ankita1 ▴ 30
0
votes
4
replies
1.8k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 7.4 years ago by 52k • written 7.4 years ago by • 0
0
votes
1
reply
1.6k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 7.5 years ago by 52k • written 7.5 years ago by • 0
11
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15
replies
3.3k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
7.5 years ago baus87 • 0
4
votes
7
replies
5.0k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 7.8 years ago by ▴ 610 • written 7.8 years ago by ▴ 10
2
votes
2
replies
1.6k
views
fdr score for degs
fdr deg
updated 7.8 years ago by ▴ 840 • written 7.8 years ago by ▴ 30
2
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3
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1.6k
views
code for up-down-regulated Degs using R
limma deg
7.9 years ago nia ▴ 30
3
votes
2
replies
1.9k
views
DEG analysis by limma
DEG Limma
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
4
votes
7
replies
1.8k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 8.2 years ago by ★ 13k • written 8.2 years ago by ▴ 20
0
votes
2
replies
1.5k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
8.9 years ago Shamim Sarhadi ▴ 20
5
votes
12
replies
2.4k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.9 years ago by ★ 7.9k • written 9.0 years ago by ▴ 20
0
votes
3
replies
1.5k
views
DEG test for two closely related conditions with limma
limma DEG
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 20
2
votes
4
replies
1.9k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 9.0 years ago by 52k • written 9.0 years ago by ▴ 20
3
votes
4
replies
4.0k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
9.5 years ago contato.carlosbau ▴ 10
3
votes
3
replies
7.6k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.0 years ago by ▴ 370 • written 10.0 years ago by • 0
47 results • Page 1 of 1
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Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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