Showing : DEG • reset
11
votes
15
replies
2.8k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
6.8 years ago • updated 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 4.8 years ago by 42k • written 4.8 years ago by • 0
5
votes
2
replies
608
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months 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 8.2 years ago by ▴ 20
4
votes
7
replies
4.4k
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
4
votes
5
replies
1.4k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.3 years ago by 50k • written 4.3 years ago by ▴ 40
4
votes
7
replies
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
3
votes
2
replies
1.6k
views
DEG analysis by limma
DEG Limma
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
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
3
votes
4
replies
3.4k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
8.7 years ago contato.carlosbau ▴ 10
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 11 months ago by 50k • written 11 months ago by • 0
3
votes
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
2
votes
3
replies
1.4k
views
code for up-down-regulated Degs using R
limma deg
7.1 years ago nia ▴ 30
2
votes
6
replies
1.5k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 4.6 years ago by 66k • written 4.6 years ago by • 0
2
votes
4
replies
1.7k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 20
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 0
2
votes
4
replies
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 5.7 years ago by • 0
2
votes
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
1
vote
0
replies
2.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.2 years ago digrigor ▴ 10
1
vote
1
reply
737
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.7 years ago by 42k • written 4.7 years ago by ▴ 20
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
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 42k • written 5.2 years ago by • 0
1
vote
3
replies
852
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
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
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 22 months ago by 66k • 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
6.2 years ago • updated 5.2 years ago SPbeginner • 0
0
votes
5
replies
1.7k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
20 months ago • updated 18 months ago marinaw ▴ 20
0
votes
3
replies
1.2k
views
DEG test for two closely related conditions with limma
limma DEG
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
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
0
votes
1
reply
1.4k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.7 years ago by 50k • written 6.7 years ago by • 0
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
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
6.3 years ago lawarde.ankita1 ▴ 30
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 66k • written 6.1 years ago by • 0
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
votes
8
replies
1.2k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
0
votes
2
replies
825
views
different designs for finding DEG by limma
limma DEG design
4.7 years ago amin.ghareyazi • 0
0
votes
0
replies
890
views
DEG among experimental and control group in MAST
MAST DEG batch effects
4.7 years ago chendianyu • 0
0
votes
4
replies
1.3k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 4.6 years ago by ★ 13k • written 4.6 years ago by • 0
0
votes
2
replies
714
views
same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
votes
1
reply
700
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 7 months ago by • 0 • written 2.8 years ago by • 0
0
votes
6
replies
3.5k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.3 years ago by 42k • written 2.3 years ago by ▴ 60
0
votes
5
replies
4.4k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 20 months ago by • 0 • written 2.2 years ago by • 0
0
votes
0
replies
246
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
0
votes
6
replies
1.4k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
22 months ago • updated 21 months ago Weiqian ▴ 10
0
votes
0
replies
723
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.0 years ago zroger499 • 0
0
votes
1
reply
629
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
47 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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