Showing : deg • reset
2
votes
4
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2.5k
views
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
3 months ago Maziya • 0
0
votes
0
replies
716
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
18 months ago Abril • 0
5
votes
2
replies
1.4k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 21 months ago by 52k • written 21 months ago by • 0
0
votes
1
reply
1.1k
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 23 months ago by • 0 • written 4.1 years ago by • 0
3
votes
11
replies
2.2k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
0
votes
1
reply
985
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
0
votes
5
replies
3.1k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
3.0 years ago • updated 2.8 years ago marinaw ▴ 20
0
votes
6
replies
2.1k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.1 years ago Weiqian ▴ 10
1
vote
7
replies
2.8k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
0
replies
1.2k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.3 years ago zroger499 • 0
0
votes
5
replies
7.2k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 3.0 years ago by • 0 • written 3.5 years ago by • 0
0
votes
6
replies
5.2k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 60
2
votes
4
replies
2.9k
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 7.0 years ago by • 0
2
votes
6
replies
6.0k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.2 years ago reganhayward • 0
3
votes
3
replies
3.1k
views
DEG analysis for Micro array affymetrix
DEG
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
1
vote
3
replies
1.3k
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
4
votes
5
replies
2.0k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 5.6 years ago by 52k • written 5.6 years ago by ▴ 40
0
votes
2
replies
1.0k
views
same results changing contrast function
deseq2 contrast DEG
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
4
replies
1.7k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 5.9 years ago by ★ 13k • written 5.9 years ago by • 0
2
votes
6
replies
2.2k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
1
vote
2
replies
2.4k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 5.9 years ago by 52k • written 5.9 years ago by • 0
0
votes
0
replies
1.2k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
6.0 years ago chendianyu • 0
0
votes
2
replies
1.1k
views
different designs for finding DEG by limma
limma DEG design
6.0 years ago amin.ghareyazi • 0
1
vote
1
reply
1.1k
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 30
5
votes
13
replies
3.9k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
8
replies
1.6k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
vote
7
replies
2.5k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
7.4 years ago • updated 6.5 years ago SPbeginner • 0
1
vote
5
replies
2.3k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
3
votes
4
replies
2.5k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 30
0
votes
0
replies
1.7k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
7.3 years ago vharshavardhanan • 0
0
votes
3
replies
2.3k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
6
votes
14
replies
3.9k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 7.4 years ago by ▴ 840 • written 7.4 years ago by ▴ 30
1
vote
0
replies
2.7k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.5 years ago digrigor ▴ 10
0
votes
0
replies
2.1k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
7.6 years ago lawarde.ankita1 ▴ 30
0
votes
4
replies
1.9k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 7.9 years ago by 52k • written 7.9 years ago by • 0
0
votes
1
reply
1.7k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 8.0 years ago by 52k • written 8.0 years ago by • 0
11
votes
15
replies
3.7k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
8.1 years ago • updated 8.0 years ago baus87 • 0
4
votes
7
replies
5.3k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 8.3 years ago by ▴ 610 • written 8.3 years ago by ▴ 10
2
votes
2
replies
1.8k
views
fdr score for degs
fdr deg
updated 8.3 years ago by ▴ 840 • written 8.3 years ago by ▴ 30
2
votes
3
replies
1.7k
views
code for up-down-regulated Degs using R
limma deg
8.4 years ago nia ▴ 30
3
votes
2
replies
2.0k
views
DEG analysis by limma
DEG Limma
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 20
4
votes
7
replies
2.0k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 8.8 years ago by ★ 13k • written 8.8 years ago by ▴ 20
0
votes
2
replies
1.6k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
9.4 years ago Shamim Sarhadi ▴ 20
5
votes
12
replies
2.7k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 9.4 years ago by ★ 7.9k • written 9.5 years ago by ▴ 20
0
votes
3
replies
1.6k
views
DEG test for two closely related conditions with limma
limma DEG
updated 9.5 years ago by ★ 29k • written 9.5 years ago by ▴ 20
2
votes
4
replies
2.1k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 9.5 years ago by 52k • written 9.5 years ago by ▴ 20
3
votes
4
replies
4.3k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
10.0 years ago contato.carlosbau ▴ 10
3
votes
3
replies
7.9k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.5 years ago by ▴ 370 • written 10.5 years ago by • 0
48 results • Page 1 of 1
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Comment: org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key by thundernight • 0
I'm actually having the same problem. [Spanish dictionary][1] [1]: https://spanishdictionary.cc
Comment: voomLmFit fitted log-CPM values by thundernight • 0
I think you may be getting confused by the differences between limma and edgeR. voomLmFit() produces a limma fitted model object so, if you…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 52k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 52k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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