Showing : DEG • reset
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
8 months ago Abril • 0
5
votes
2
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982
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 11 months ago by 51k • written 11 months ago by • 0
0
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1
reply
862
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 13 months ago by • 0 • written 3.3 years ago by • 0
3
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11
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1.7k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 16 months ago by 51k • written 16 months ago by • 0
0
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1
reply
801
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 19 months ago by 51k • written 19 months ago by • 0
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5
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2.3k
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Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
2.1 years ago • updated 2.0 years ago marinaw ▴ 20
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6
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1.7k
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
2.3 years ago Weiqian ▴ 10
1
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7
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2.1k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
0
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0
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917
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.5 years ago zroger499 • 0
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5
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5.6k
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DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
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6
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4.2k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.8 years ago by 42k • written 2.8 years ago by ▴ 60
2
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4
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2.6k
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 6.2 years ago by • 0
2
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6
replies
5.2k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.4 years ago reganhayward • 0
3
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3
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2.5k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
1
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3
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1.0k
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DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.7 years ago by 42k • written 4.7 years ago by • 0
4
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5
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1.6k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.7 years ago by 51k • written 4.8 years ago by ▴ 40
0
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2
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849
views
same results changing contrast function
deseq2 contrast DEG
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
0
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4
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1.5k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 5.1 years ago by ★ 13k • written 5.1 years ago by • 0
2
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6
replies
1.8k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 5.1 years ago by 67k • written 5.1 years ago by • 0
1
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2
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1.9k
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Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 5.1 years ago by 51k • written 5.1 years ago by • 0
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0
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1.0k
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DEG among experimental and control group in MAST
MAST DEG batch effects
5.1 years ago chendianyu • 0
0
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2
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931
views
different designs for finding DEG by limma
limma DEG design
5.2 years ago amin.ghareyazi • 0
1
vote
1
reply
872
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 5.2 years ago by 42k • written 5.2 years ago by ▴ 30
5
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13
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3.1k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
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8
replies
1.3k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
1
vote
7
replies
2.1k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
6.6 years ago • updated 5.7 years ago SPbeginner • 0
1
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5
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2.0k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
3
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4
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2.0k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 5.9 years ago by 51k • written 5.9 years ago by ▴ 30
0
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0
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1.5k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.5 years ago vharshavardhanan • 0
0
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3
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2.0k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.6 years ago by 67k • written 6.6 years ago by • 0
6
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14
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3.3k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 6.6 years ago by ▴ 830 • written 6.6 years ago by ▴ 30
1
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0
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2.4k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.6 years ago digrigor ▴ 10
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0
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1.8k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
6.7 years ago lawarde.ankita1 ▴ 30
0
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4
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1.7k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 7.1 years ago by 51k • written 7.1 years ago by • 0
0
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1
reply
1.5k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 7.1 years ago by 51k • written 7.1 years ago by • 0
11
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15
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3.1k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
7.2 years ago baus87 • 0
4
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7
replies
4.7k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 7.5 years ago by ▴ 610 • written 7.5 years ago by ▴ 10
2
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2
replies
1.4k
views
fdr score for degs
fdr deg
updated 7.5 years ago by ▴ 830 • written 7.5 years ago by ▴ 30
2
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3
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1.5k
views
code for up-down-regulated Degs using R
limma deg
7.6 years ago nia ▴ 30
3
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2
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1.7k
views
DEG analysis by limma
DEG Limma
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
4
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7
replies
1.7k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 7.9 years ago by ★ 13k • written 7.9 years ago by ▴ 20
0
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2
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1.4k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
8.6 years ago Shamim Sarhadi ▴ 20
5
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12
replies
2.2k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 20
0
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3
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1.4k
views
DEG test for two closely related conditions with limma
limma DEG
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 20
2
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4
replies
1.8k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.7 years ago by 51k • written 8.7 years ago by ▴ 20
3
votes
4
replies
3.8k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
9.2 years ago • updated 9.1 years ago contato.carlosbau ▴ 10
3
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3
replies
7.3k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.7 years ago by ▴ 370 • written 9.7 years ago by • 0
47 results • Page 1 of 1
Recent ...
Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: ESTMATE, MCPcounter, EPIC, xCell input by Kang • 0
These are not, as far as I know, bioconductor packages. You should query on the websites for those specific software programs. @[mapquest][…
Comment: Robust way of dealing with low number of samples for Differential Gene Expressio by Kang • 0
I believe that pseudo-bulking is a strong way to approach DE, as long as it is possible to reliably identify the cell type across data and …
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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