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Showing :
DEG
•
reset
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
b.nota
▴ 360 • written 9.2 years ago by
Yue Zhao
• 0
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
2.9 years ago
reganhayward
• 0
0
votes
5
replies
4.4k
views
DESeq2/Differential expression analysis without replicates
DESeq2
DEG
updated 20 months ago by
bioinfomagics
• 0 • written 2.2 years ago by
priya.dalvi
• 0
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
Bernd Klaus
▴ 610 • written 7.0 years ago by
Maximilian
▴ 10
0
votes
6
replies
3.5k
views
Performing simple pairwise comparisons in DESEQ2
edgeR
DEG
RNASeq
DESEQ2
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
Raito92
▴ 60
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
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
svlachavas
▴ 830 • written 6.1 years ago by
lawarde.ankita1
▴ 30
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
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
Michael Love
42k • written 4.8 years ago by
amin.ghareyazi
• 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
Biomed
• 0
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
3
votes
3
replies
2.1k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
sheikhbeigali
• 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
Ryan C. Thompson
★ 7.9k • written 8.2 years ago by
Shamim Sarhadi
▴ 20
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 5.2 years ago
SPbeginner
• 0
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
James W. MacDonald
66k • written 6.1 years ago by
amy16
• 0
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
Michael Love
42k • written 5.2 years ago by
hermanapis
• 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
Gordon Smyth
50k • written 5.4 years ago by
rproendo
▴ 20
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
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
Gordon Smyth
50k • written 8.2 years ago by
Shamim Sarhadi
▴ 20
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics
DESeq2
DEGreport
RNASeqData
DEG
updated 22 months ago by
James W. MacDonald
66k • written 22 months ago by
Diya
• 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
3
votes
2
replies
1.6k
views
DEG analysis by limma
DEG
Limma
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
Shamim Sarhadi
▴ 20
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
Gordon Smyth
50k • written 4.6 years ago by
kawess
• 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
Gordon Smyth
50k • written 6.6 years ago by
JackieMe
• 0
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
James W. MacDonald
66k • written 4.6 years ago by
mjavad2012
• 0
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
Steve Lianoglou
★ 13k • written 7.5 years ago by
Shamim Sarhadi
▴ 20
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
Gordon Smyth
50k • written 4.3 years ago by
Pietro
▴ 40
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
2
votes
3
replies
1.4k
views
code for up-down-regulated Degs using R
limma
deg
7.1 years ago
nia
▴ 30
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
Gordon Smyth
50k • written 11 months ago by
alexia.brunel
• 0
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
6.0 years ago
vharshavardhanan
• 0
0
votes
1
reply
1.4k
views
RNA-Seq DEG analysis questions
rnaseq
deg
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
mullin.yu
• 0
0
votes
4
replies
1.3k
views
DESeq2 analysis with multiple factors
DESeq2
DEG
multiplefactors
deseq2
updated 4.6 years ago by
Steve Lianoglou
★ 13k • written 4.6 years ago by
yura.song
• 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
svlachavas
▴ 830 • written 7.0 years ago by
nia
▴ 30
0
votes
3
replies
1.2k
views
DEG test for two closely related conditions with limma
limma
DEG
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Shamim Sarhadi
▴ 20
0
votes
8
replies
1.2k
views
Custom post-normalization counts from DESeq2
DEG
deseq2
Covariate
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
sum732
• 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
1
vote
3
replies
852
views
DESeq2 - controlling for other variables
deseq2
DEG
covariate
study design
variables
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
Yonatan Amzaleg
• 0
0
votes
2
replies
825
views
different designs for finding DEG by limma
limma
DEG
design
4.7 years ago
amin.ghareyazi
• 0
1
vote
1
reply
737
views
DeSeq RNASeq differential expression between region samples
R
deseq2
DEG
updated 4.7 years ago by
Michael Love
42k • written 4.7 years ago by
ecg1g15
▴ 20
0
votes
0
replies
722
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
2
replies
714
views
same results changing contrast function
deseq2
contrast
DEG
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
ire.ontiveros
• 0
0
votes
1
reply
699
views
Multiple groups comparison using Linnorm
Linnorm
DEG
MultipleComparison
updated 7 months ago by
shunyip
• 0 • written 2.8 years ago by
awakumaya
• 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
Gordon Smyth
50k • written 13 months ago by
Ankita
• 0
5
votes
2
replies
607
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
0
votes
0
replies
246
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
3 months ago
Abril
• 0
47 results • Page
1 of 1
Recent ...
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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.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
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
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
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