Showing : DEG • reset
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
4 months ago Abril • 0
5
votes
2
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675
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 6 months ago by 51k • written 6 months ago by • 0
0
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1
reply
717
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 8 months ago by • 0 • written 2.9 years ago by • 0
3
votes
11
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1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 11 months ago by 51k • written 11 months ago by • 0
0
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1
reply
666
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Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 14 months ago by 51k • written 14 months ago by • 0
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5
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1.8k
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Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
21 months ago • updated 19 months ago marinaw ▴ 20
0
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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
22 months ago Weiqian ▴ 10
1
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7
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1.7k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 23 months ago by 66k • written 23 months ago by • 0
0
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0
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745
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.1 years ago zroger499 • 0
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5
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4.6k
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DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 21 months ago by • 0 • written 2.3 years ago by • 0
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6
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3.6k
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Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.4 years ago by 42k • written 2.4 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 5.8 years ago by • 0
2
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6
replies
4.7k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.0 years ago reganhayward • 0
3
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3
replies
2.1k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
1
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3
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878
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DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.3 years ago by 42k • written 4.3 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 51k • written 4.4 years ago by ▴ 40
0
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2
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734
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same results changing contrast function
deseq2 contrast DEG
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
0
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4
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1.3k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 4.7 years ago by ★ 13k • written 4.7 years ago by • 0
2
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6
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1.5k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 4.7 years ago by 66k • written 4.7 years ago by • 0
1
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2
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1.6k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 4.7 years ago by 51k • written 4.7 years ago by • 0
0
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0
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910
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.7 years ago chendianyu • 0
0
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2
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834
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different designs for finding DEG by limma
limma DEG design
4.8 years ago amin.ghareyazi • 0
1
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1
reply
754
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.8 years ago by 42k • written 4.8 years ago by ▴ 20
5
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13
replies
2.8k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
0
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8
replies
1.2k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
1
vote
7
replies
1.9k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
6.2 years ago • updated 5.3 years ago SPbeginner • 0
1
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5
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1.8k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
1
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4
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1.8k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 5.5 years ago by 51k • written 5.5 years ago by ▴ 20
0
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0
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1.4k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.1 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 6.2 years ago by 66k • written 6.2 years ago by • 0
6
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14
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3.0k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 6.2 years ago by ▴ 830 • written 6.2 years ago by ▴ 30
1
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0
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2.1k
views
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
6.3 years ago lawarde.ankita1 ▴ 30
0
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4
replies
1.5k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 6.7 years ago by 51k • written 6.7 years ago by • 0
0
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1
reply
1.4k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.7 years ago by 51k • written 6.7 years ago by • 0
11
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15
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2.8k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
6.8 years ago baus87 • 0
4
votes
7
replies
4.4k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 7.1 years ago by ▴ 610 • written 7.1 years ago by ▴ 10
2
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2
replies
1.3k
views
fdr score for degs
fdr deg
updated 7.1 years ago by ▴ 830 • written 7.1 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
7.2 years ago nia ▴ 30
3
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2
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1.6k
views
DEG analysis by limma
DEG Limma
updated 7.5 years ago by ★ 28k • written 7.5 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 7.5 years ago by ★ 13k • written 7.5 years ago by ▴ 20
0
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2
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1.3k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
8.2 years ago Shamim Sarhadi ▴ 20
5
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12
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2.0k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.2 years ago by ★ 7.9k • written 8.2 years ago by ▴ 20
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3
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1.3k
views
DEG test for two closely related conditions with limma
limma DEG
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 20
2
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4
replies
1.7k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.3 years ago by 51k • written 8.3 years ago by ▴ 20
3
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4
replies
3.5k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
8.8 years ago • updated 8.7 years ago contato.carlosbau ▴ 10
3
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3
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6.9k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.3 years ago by ▴ 360 • written 9.3 years ago by • 0
47 results • Page 1 of 1
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Replies
Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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