Showing : deg • reset
11
votes
15
replies
3.4k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
7.6 years ago baus87 • 0
3
votes
4
replies
4.0k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
9.5 years ago contato.carlosbau ▴ 10
2
votes
3
replies
1.6k
views
code for up-down-regulated Degs using R
limma deg
8.0 years ago nia ▴ 30
2
votes
4
replies
1.9k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 9.0 years ago by 52k • written 9.0 years ago by ▴ 20
6
votes
14
replies
3.6k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 7.0 years ago by ▴ 840 • written 7.0 years ago by ▴ 30
2
votes
4
replies
2.7k
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 6.5 years ago by • 0
3
votes
4
replies
2.2k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 30
4
votes
7
replies
5.0k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 7.8 years ago by ▴ 610 • written 7.8 years ago by ▴ 10
5
votes
12
replies
2.4k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 9.0 years ago by ★ 7.9k • written 9.0 years ago by ▴ 20
5
votes
2
replies
1.2k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 15 months ago by 52k • written 15 months ago by • 0
4
votes
5
replies
1.8k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 5.1 years ago by 52k • written 5.1 years ago by ▴ 40
3
votes
11
replies
2.0k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 21 months ago by 52k • written 21 months ago by • 0
0
votes
8
replies
1.5k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
5
votes
13
replies
3.5k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
1
vote
1
reply
984
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 30
0
votes
5
replies
2.7k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
2.5 years ago • updated 2.4 years ago marinaw ▴ 20
3
votes
3
replies
7.7k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.0 years ago by ▴ 370 • written 10.0 years ago by • 0
0
votes
3
replies
1.5k
views
DEG test for two closely related conditions with limma
limma DEG
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 20
0
votes
2
replies
1.5k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
9.0 years ago Shamim Sarhadi ▴ 20
4
votes
7
replies
1.8k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 8.3 years ago by ★ 13k • written 8.3 years ago by ▴ 20
3
votes
2
replies
1.9k
views
DEG analysis by limma
DEG Limma
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 20
2
votes
2
replies
1.6k
views
fdr score for degs
fdr deg
updated 7.9 years ago by ▴ 840 • written 7.9 years ago by ▴ 30
0
votes
1
reply
1.6k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 7.5 years ago by 52k • written 7.5 years ago by • 0
0
votes
4
replies
1.8k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 7.4 years ago by 52k • written 7.4 years ago by • 0
1
vote
7
replies
2.3k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
7.0 years ago • updated 6.0 years ago SPbeginner • 0
0
votes
3
replies
2.2k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
1
vote
5
replies
2.1k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
954
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 17 months ago by • 0 • written 3.6 years ago by • 0
0
votes
6
replies
4.8k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 60
0
votes
5
replies
6.4k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 2.5 years ago by • 0 • written 3.1 years ago by • 0
0
votes
6
replies
1.9k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
2.6 years ago Weiqian ▴ 10
2
votes
6
replies
5.7k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.8 years ago • updated 3.7 years ago reganhayward • 0
1
vote
7
replies
2.5k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
votes
1
reply
885
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 23 months ago by 52k • written 23 months ago by • 0
1
vote
2
replies
2.2k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 5.5 years ago by 52k • written 5.5 years ago by • 0
2
votes
6
replies
2.0k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
0
votes
4
replies
1.6k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 5.4 years ago by ★ 13k • written 5.4 years ago by • 0
0
votes
2
replies
929
views
same results changing contrast function
deseq2 contrast DEG
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
3
replies
1.1k
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 5.0 years ago by 43k • written 5.1 years ago by • 0
3
votes
3
replies
2.8k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
votes
0
replies
1.1k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
5.5 years ago chendianyu • 0
0
votes
0
replies
1.1k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.9 years ago zroger499 • 0
0
votes
0
replies
1.9k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
7.1 years ago lawarde.ankita1 ▴ 30
0
votes
0
replies
1.6k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.9 years ago vharshavardhanan • 0
1
vote
0
replies
2.5k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.0 years ago digrigor ▴ 10
0
votes
2
replies
1.0k
views
different designs for finding DEG by limma
limma DEG design
5.6 years ago amin.ghareyazi • 0
0
votes
0
replies
601
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
13 months ago Abril • 0
47 results • Page 1 of 1
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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step. You don't need a con…
Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
Answer: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa by Daniel • 0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Votes
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
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