Showing : DEG • reset
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 weeks ago Abril • 0
5
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2
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544
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
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1
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683
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Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 6 months ago by • 0 • written 2.8 years ago by • 0
3
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11
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1.3k
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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
602
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Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 12 months ago by 50k • written 13 months ago by • 0
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5
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1.6k
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Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
19 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
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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
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0
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703
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
24 months ago zroger499 • 0
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5
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4.3k
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DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 19 months ago by • 0 • written 2.2 years ago by • 0
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6
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3.4k
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Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.2 years ago by 41k • written 2.2 years ago by ▴ 60
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4
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2.3k
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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 5.6 years ago by • 0
2
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6
replies
4.5k
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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2.0k
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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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836
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DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
4
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5
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1.4k
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All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 40
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2
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704
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same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 41k • 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 4.5 years ago by ★ 13k • written 4.5 years ago by • 0
2
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6
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1.4k
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"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 4.5 years ago by 65k • written 4.5 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
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0
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875
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
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2
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810
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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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726
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DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 20
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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 41k • written 4.7 years ago by • 0
0
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8
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1.1k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.0 years ago by 41k • 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 5.1 years ago SPbeginner • 0
1
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5
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1.7k
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Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.2 years ago by 41k • 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 5.3 years ago by 50k • written 5.4 years ago by ▴ 20
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0
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1.3k
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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
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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
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14
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2.9k
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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
6.1 years ago digrigor ▴ 10
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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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1.3k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.6 years ago by 50k • written 6.6 years ago by • 0
11
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15
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2.7k
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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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4.3k
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Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 6.9 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
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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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1.4k
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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
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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 8.1 years ago by ▴ 20
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3
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1.2k
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DEG test for two closely related conditions with limma
limma DEG
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 20
2
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4
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1.6k
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A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.1 years ago by 50k • written 8.1 years ago by ▴ 20
3
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4
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3.4k
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R Script for selecting differentially expressed genes
limma microarray affy deg
8.7 years ago • updated 8.6 years ago contato.carlosbau ▴ 10
3
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3
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6.8k
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Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.1 years ago by ▴ 360 • written 9.1 years ago by • 0
47 results • Page 1 of 1
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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