Showing : DEG • reset
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
5
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2
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596
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
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1
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696
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Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 7 months ago by • 0 • written 2.8 years ago by • 0
3
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11
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1.4k
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SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 10 months ago by • 0
0
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1
reply
623
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Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 13 months ago by 50k • written 13 months ago by • 0
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5
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1.7k
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Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
20 months ago • updated 18 months ago marinaw ▴ 20
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6
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1.4k
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
21 months ago Weiqian ▴ 10
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
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0
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718
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.0 years ago zroger499 • 0
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5
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4.4k
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DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 20 months ago by • 0 • written 2.2 years ago by • 0
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6
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3.5k
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Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.3 years ago by 42k • written 2.3 years ago by ▴ 60
2
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4
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2.4k
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 5.7 years ago by • 0
2
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6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 0
3
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3
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2.1k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
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3
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849
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DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
4
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5
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1.4k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.3 years ago by 50k • written 4.3 years ago by ▴ 40
0
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2
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713
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same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
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4
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1.3k
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DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 4.6 years ago by ★ 13k • written 4.6 years ago by • 0
2
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6
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1.5k
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"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 4.6 years ago by 65k • written 4.6 years ago by • 0
1
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2
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1.5k
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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 4.6 years ago by 50k • written 4.6 years ago by • 0
0
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0
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884
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
0
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2
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823
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different designs for finding DEG by limma
limma DEG design
4.7 years ago amin.ghareyazi • 0
1
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1
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735
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DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.7 years ago by 42k • written 4.7 years ago by ▴ 20
5
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13
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2.7k
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DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 4.7 years ago by 42k • written 4.7 years ago by • 0
0
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8
replies
1.2k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
1
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7
replies
1.9k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
6.1 years ago • updated 5.2 years ago SPbeginner • 0
1
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5
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1.7k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
1
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4
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1.7k
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Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 20
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0
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1.4k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
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3
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1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.1 years ago by 65k • written 6.1 years ago by • 0
6
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14
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3.0k
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Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 6.1 years ago by ▴ 830 • written 6.1 years ago by ▴ 30
1
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0
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2.1k
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topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.2 years ago digrigor ▴ 10
0
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0
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1.6k
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Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
6.2 years ago lawarde.ankita1 ▴ 30
0
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4
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1.5k
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Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 6.6 years ago by 50k • written 6.6 years ago by • 0
0
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1
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1.4k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.7 years ago by 50k • written 6.7 years ago by • 0
11
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15
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2.8k
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edgeR - MDS Plot for Count Data
edger DEG mds plot
6.7 years ago baus87 • 0
4
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7
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4.4k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 7.0 years ago by ▴ 610 • written 7.0 years ago by ▴ 10
2
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2
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1.3k
views
fdr score for degs
fdr deg
updated 7.0 years ago by ▴ 830 • written 7.0 years ago by ▴ 30
2
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3
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1.4k
views
code for up-down-regulated Degs using R
limma deg
7.1 years ago nia ▴ 30
3
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2
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1.5k
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DEG analysis by limma
DEG Limma
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
4
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7
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1.5k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 7.4 years ago by ★ 13k • written 7.4 years ago by ▴ 20
0
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2
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1.3k
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Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
8.1 years ago Shamim Sarhadi ▴ 20
5
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12
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1.9k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.1 years ago by ★ 7.9k • written 8.2 years ago by ▴ 20
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3
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1.2k
views
DEG test for two closely related conditions with limma
limma DEG
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
2
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4
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1.7k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 20
3
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4
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3.4k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
8.7 years ago contato.carlosbau ▴ 10
3
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3
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6.8k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.2 years ago by ▴ 360 • written 9.2 years ago by • 0
47 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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