Showing : DEG • reset
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Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
8 weeks ago awakumaya • 0
2
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4
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1.2k
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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 3.0 years ago by • 0
2
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6
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307
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Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3 months ago reganhayward • 0
3
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3
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299
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DEG analysis for Micro array affymetrix
DEG
updated 17 months ago by 3.4k • written 17 months ago by • 0
1
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3
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194
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DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 19 months ago by 34k • written 19 months ago by • 0
4
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5
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369
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All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 19 months ago by 43k • written 19 months ago by ▴ 30
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2
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201
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same results changing contrast function
deseq2 contrast DEG
updated 22 months ago by 34k • written 22 months ago by • 0
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4
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318
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DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 23 months ago by 13k • written 23 months ago by • 0
2
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6
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357
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"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 23 months ago by 58k • written 23 months ago by • 0
1
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2
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484
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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 24 months ago by 43k • written 24 months ago by • 0
0
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0
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278
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DEG among experimental and control group in MAST
MAST DEG batch effects
2.0 years ago chendianyu • 0
0
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2
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282
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different designs for finding DEG by limma
limma DEG design
2.1 years ago amin.ghareyazi • 0
1
vote
1
reply
201
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DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 2.1 years ago by 34k • written 2.1 years ago by • 0
5
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13
replies
765
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DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 2.1 years ago by 34k • written 2.1 years ago by • 0
0
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8
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358
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Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 2.4 years ago by 34k • written 2.4 years ago by • 0
1
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7
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971
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limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
3.5 years ago • updated 2.5 years ago SPbeginner • 0
1
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5
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526
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Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 2.6 years ago by 34k • written 2.6 years ago by • 0
1
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4
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685
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Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 2.7 years ago by 43k • written 2.8 years ago by ▴ 20
0
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0
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616
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Ballgown data processing error
Ballgown Stringtie DEG rnaseq
3.4 years ago vharshavardhanan • 0
0
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3
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907
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Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 3.5 years ago by 58k • written 3.5 years ago by • 0
6
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14
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1.4k
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Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by ▴ 20
1
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0
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831
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topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
3.5 years ago digrigor ▴ 10
0
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0
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841
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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
3.6 years ago lawarde.ankita1 ▴ 20
0
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4
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619
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Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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1
reply
713
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RNA-Seq DEG analysis questions
rnaseq deg
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
11
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15
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1.5k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
4.1 years ago baus87 • 0
4
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7
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2.1k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 4.4 years ago by ▴ 600 • written 4.4 years ago by ▴ 10
2
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2
replies
648
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fdr score for degs
fdr deg
updated 4.4 years ago by ▴ 780 • written 4.4 years ago by ▴ 30
2
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3
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792
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code for up-down-regulated Degs using R
limma deg
4.5 years ago nia ▴ 30
3
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2
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888
views
DEG analysis by limma
DEG Limma
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 20
4
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7
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734
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DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 4.8 years ago by 13k • written 4.8 years ago by ▴ 20
0
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2
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614
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Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
5.5 years ago Shamim Sarhadi ▴ 20
5
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12
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1.1k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 5.5 years ago by 7.6k • written 5.5 years ago by ▴ 20
0
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3
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716
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DEG test for two closely related conditions with limma
limma DEG
updated 5.5 years ago by ★ 27k • written 5.5 years ago by ▴ 20
2
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4
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853
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A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 20
3
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4
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2.2k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
6.1 years ago • updated 6.0 years ago contato.carlosbau ▴ 10
3
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3
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4.7k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 6.5 years ago by ▴ 340 • written 6.6 years ago by • 0
37 results • Page 1 of 1
Recent ...
Replies
Comment: Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dat by IIart.hubII • 0
What is "coad_clear" in this case? What data have you allotted to it? Can you please share the whole code? Or can anyone answer this questi…
Comment: GenomicScores package: availableGScores and getGScores functions not working by Robert Castelo ★ 2.7k
hi, Indeed you were using an outdated version of the package. Regarding how to install current release version, please read first carefull…
Answer: Unable to install Bioconductor packages by shepherl 2.8k
This normally occurs when R was installed with a different account or an admin account. Unless on this account you won't be able to update…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
I tried to install the latest version of GenomicScores (2.4.0) by downloading the tar.gz and running `install.packages('GenomicScores_2.4.0…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
Thanks for the quick response. Below is my sessionInfo R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) …
Votes
A: Differential expression analysis starting from TPM data
Comment: deseq2 machine sizing best practices for very large data set
Comment: Extracting normalized counts in MEDIPS
Comment: "full model matrix is less than full rank"
A: Extracting normalized counts in MEDIPS
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