Showing : deg • reset
11
votes
15
replies
2.8k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
6.7 years ago baus87 • 0
6
votes
14
replies
3.0k
views
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
5
votes
13
replies
2.7k
views
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
5
votes
12
replies
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
3
votes
11
replies
1.3k
views
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
votes
8
replies
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
4
votes
7
replies
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
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 21 months ago by 65k • written 22 months ago by • 0
1
vote
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
4
votes
7
replies
4.3k
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
0
votes
6
replies
3.4k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.2 years ago by 41k • written 2.3 years ago by ▴ 60
2
votes
6
replies
4.5k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 0
0
votes
6
replies
1.4k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
21 months ago Weiqian ▴ 10
2
votes
6
replies
1.4k
views
"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
0
votes
5
replies
1.7k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
19 months ago • updated 18 months ago marinaw ▴ 20
1
vote
5
replies
1.7k
views
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
4
votes
5
replies
1.4k
views
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
0
votes
5
replies
4.3k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 19 months ago by • 0 • written 2.2 years ago by • 0
2
votes
4
replies
1.6k
views
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
0
votes
4
replies
1.3k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 4.5 years ago by ★ 13k • written 4.5 years ago by • 0
2
votes
4
replies
2.3k
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
1
vote
4
replies
1.7k
views
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
0
votes
4
replies
1.5k
views
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
3
votes
4
replies
3.4k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
8.7 years ago • updated 8.6 years ago contato.carlosbau ▴ 10
0
votes
3
replies
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
3
votes
3
replies
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
2
votes
3
replies
1.4k
views
code for up-down-regulated Degs using R
limma deg
7.1 years ago nia ▴ 30
1
vote
3
replies
842
views
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
3
votes
3
replies
2.0k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
0
votes
3
replies
1.2k
views
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
5
votes
2
replies
557
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 5 months ago by • 0
0
votes
2
replies
710
views
same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
0
votes
2
replies
1.3k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
8.1 years ago Shamim Sarhadi ▴ 20
2
votes
2
replies
1.3k
views
fdr score for degs
fdr deg
updated 7.0 years ago by ▴ 830 • written 7.0 years ago by ▴ 30
1
vote
2
replies
1.5k
views
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
votes
2
replies
814
views
different designs for finding DEG by limma
limma DEG design
4.7 years ago amin.ghareyazi • 0
3
votes
2
replies
1.5k
views
DEG analysis by limma
DEG Limma
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
0
votes
1
reply
610
views
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
0
votes
1
reply
1.3k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.6 years ago by 50k • written 6.6 years ago by • 0
0
votes
1
reply
687
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 6 months ago by • 0 • written 2.8 years ago by • 0
1
vote
1
reply
730
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 20
0
votes
0
replies
706
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
24 months ago zroger499 • 0
0
votes
0
replies
1.6k
views
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
1
vote
0
replies
2.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.1 years ago digrigor ▴ 10
0
votes
0
replies
224
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 weeks ago Abril • 0
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
votes
0
replies
879
views
DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
47 results • Page 1 of 1
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Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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