Showing : DEG • reset
3
votes
11
replies
799
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 3 months ago by 48k • written 3 months ago by • 0
0
votes
1
reply
313
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 5 months ago by 48k • written 5 months ago by • 0
0
votes
5
replies
891
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
12 months ago • updated 10 months ago marinaw ▴ 20
0
votes
6
replies
958
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
14 months ago • updated 13 months ago Weiqian ▴ 10
1
vote
7
replies
979
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 14 months ago by 63k • written 14 months ago by • 0
0
votes
0
replies
476
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
16 months ago zroger499 • 0
0
votes
5
replies
2.9k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 12 months ago by • 0 • written 19 months ago by • 0
0
votes
6
replies
2.5k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 19 months ago by 40k • written 19 months ago by ▴ 60
0
votes
0
replies
415
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
2.2 years ago awakumaya • 0
2
votes
4
replies
2.0k
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 5.0 years ago by • 0
2
votes
6
replies
3.8k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.3 years ago reganhayward • 0
3
votes
3
replies
1.4k
views
DEG analysis for Micro array affymetrix
DEG
updated 3.4 years ago by 3.8k • written 3.4 years ago by • 0
1
vote
3
replies
607
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 3.6 years ago by 40k • written 3.6 years ago by • 0
4
votes
5
replies
1.1k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 3.6 years ago by 48k • written 3.6 years ago by ▴ 40
0
votes
2
replies
546
views
same results changing contrast function
deseq2 contrast DEG
updated 3.9 years ago by 40k • written 3.9 years ago by • 0
0
votes
4
replies
1.1k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 3.9 years ago by 13k • written 3.9 years ago by • 0
2
votes
6
replies
1.1k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 3.9 years ago by 63k • written 3.9 years ago by • 0
1
vote
2
replies
1.1k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 4.0 years ago by 48k • written 4.0 years ago by • 0
0
votes
0
replies
669
views
DEG among experimental and control group in MAST
MAST DEG batch effects
4.0 years ago chendianyu • 0
0
votes
2
replies
635
views
different designs for finding DEG by limma
limma DEG design
4.1 years ago amin.ghareyazi • 0
1
vote
1
reply
540
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.1 years ago by 40k • written 4.1 years ago by ▴ 20
5
votes
13
replies
2.1k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 4.1 years ago by 40k • written 4.1 years ago by • 0
0
votes
8
replies
832
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 4.3 years ago by 40k • written 4.4 years ago by • 0
1
vote
7
replies
1.6k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
5.5 years ago • updated 4.5 years ago SPbeginner • 0
1
vote
5
replies
1.4k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 4.6 years ago by 40k • written 4.6 years ago by • 0
1
vote
4
replies
1.4k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 4.7 years ago by 48k • written 4.7 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
5.4 years ago vharshavardhanan • 0
0
votes
3
replies
1.6k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 5.5 years ago by 63k • written 5.5 years ago by • 0
6
votes
14
replies
2.4k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 5.5 years ago by ▴ 810 • written 5.5 years ago by ▴ 30
1
vote
0
replies
1.7k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
5.5 years ago digrigor ▴ 10
0
votes
0
replies
1.4k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
5.6 years ago lawarde.ankita1 ▴ 30
0
votes
4
replies
1.1k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 6.0 years ago by 48k • written 6.0 years ago by • 0
0
votes
1
reply
1.1k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.0 years ago by 48k • written 6.0 years ago by • 0
11
votes
15
replies
2.4k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
6.1 years ago baus87 • 0
4
votes
7
replies
3.8k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 6.3 years ago by ▴ 610 • written 6.4 years ago by ▴ 10
2
votes
2
replies
1.0k
views
fdr score for degs
fdr deg
updated 6.4 years ago by ▴ 810 • written 6.4 years ago by ▴ 30
2
votes
3
replies
1.2k
views
code for up-down-regulated Degs using R
limma deg
6.5 years ago nia ▴ 30
3
votes
2
replies
1.3k
views
DEG analysis by limma
DEG Limma
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 20
4
votes
7
replies
1.2k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 6.8 years ago by 13k • written 6.8 years ago by ▴ 20
0
votes
2
replies
1.1k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
7.5 years ago Shamim Sarhadi ▴ 20
5
votes
12
replies
1.6k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 7.5 years ago by 7.8k • written 7.5 years ago by ▴ 20
0
votes
3
replies
1.1k
views
DEG test for two closely related conditions with limma
limma DEG
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
2
votes
4
replies
1.3k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 7.5 years ago by 48k • written 7.5 years ago by ▴ 20
3
votes
4
replies
3.0k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
8.0 years ago contato.carlosbau ▴ 10
3
votes
3
replies
6.2k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 8.5 years ago by ▴ 360 • written 8.5 years ago by • 0
45 results • Page 1 of 1
Recent ...
Replies
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
No. But I will need to modify the `write_block()` method for TENxRealizationSink implemented in **HDF5Array** to make it handle blocks that…
Answer: ''Model_Matrix'' error by Gordon Smyth 48k
This is actually an error message from base R rather than from limma. The error says that `Group` contains 0 or 1 levels, so your assumptio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I don't know the details but do you mean using HDF5RealizationSink or TENxRealizationSink will make it possible to writing sparse multi-d…
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Awards • All
Popular Question to Gordon Smyth 48k
Popular Question to Hervé Pagès 16k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to sohail.mbio ▴ 10
Popular Question to komal.rathi ▴ 110
Locations • All
WEHI, Melbourne, Australia, just now
Seattle, WA, United States, 15 minutes ago
Germany, 17 minutes ago
The city by the bay, 49 minutes ago
United States, 53 minutes ago
Traffic: 374 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6