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Gene expression
•
reset
7
votes
13
replies
2.3k
views
Test whether expression levels of two gene sets are significantly different
R
DESeq2
gene set testing
gene expression
7.5 years ago
Jon Bråte
▴ 250
0
votes
4
replies
1.3k
views
Gene clusters based on gene expression across samples
kmeans
gene expression
clustering
6.6 years ago • updated 6.5 years ago
Jane Merlevede
▴ 90
9
votes
6
replies
1.8k
views
Representative gene expression value in one condition with several replicates
rnaseq
gene expression
edger
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
Jack
• 0
1
vote
3
replies
1.7k
views
RPM data analysis with DESeq2
deseq2
RPM
gene expression
5.1 years ago
ruhollah.mb
• 0
3
votes
3
replies
1.9k
views
Differential Expression Analysis in edgeR using Anova
edger
anova
gene expression
Dispersion
updated 4.9 years ago by
onlychainsaw2019
• 0 • written 5.3 years ago by
ilovesuperheroes1993
• 0
2
votes
2
replies
1.4k
views
SAM/siggenes: Differential gene expression analysis
SAM
siggenes
microarray
gene expression
sam
7.3 years ago
Brian Smith
▴ 120
0
votes
4
replies
1.3k
views
limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of…
limma
gene expression
differential gene expression
6.5 years ago
arfranco
▴ 130
0
votes
2
replies
842
views
Is there any bioc tool to predict/quantify transcription factor activation using gene expression data?
transcription factor
tf activation
gene regulatory network
gene expression
updated 7.4 years ago by
caroline.green.c91
• 0 • written 7.4 years ago by
Diwan
• 0
0
votes
7
replies
1.3k
views
How to read Illumina data used in the MACQ project (GSE5350)
microarray
normalization
Illumina data
MACQ project
gene expression
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
naf
• 0
0
votes
2
replies
1.1k
views
DESeq2 # of up-and down-regulated genes are approximately equal
deseq2
gene expression
updated 3.6 years ago by
Michael Love
42k • written 3.6 years ago by
sorrymouse
• 0
0
votes
2
replies
3.0k
views
barplot with ggplot2 for gene expression
ggplot2
barplot
gene expression
gene expression
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
alakatos
▴ 130
0
votes
2
replies
1.2k
views
Help needed to identify common genes among datasets
datasets
genes
gene expression
updated 8.7 years ago by
Steve Lianoglou
★ 13k • written 8.7 years ago by
vavecilla
• 0
0
votes
3
replies
1.4k
views
Anova test on gene expression data
Anova
gene expression
updated 6.5 years ago by
James W. MacDonald
65k • written 6.5 years ago by
sally_b86
• 0
1
vote
1
reply
6.3k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna
clustering
gene expression
updated 7.1 years ago by
Peter Langfelder
★ 3.0k • written 7.1 years ago by
ngeraci
▴ 10
2
votes
1
reply
1.0k
views
gene expression data analysis and batch effect methods
batch effect
gene expression
updated 7.0 years ago by
chris86
▴ 420 • written 7.0 years ago by
tati6406
• 0
1
vote
3
replies
2.4k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi
geoquery
geo
illumina human ht-12 v4
gene expression
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
aaronrosenstein
• 0
0
votes
2
replies
1.7k
views
How can I compare the expression of two genes within the same sample?
gene expression
rnaseq
deseq2
updated 5.4 years ago by
heyao
▴ 30 • written 5.4 years ago by
chiara.facciotto
• 0
2
votes
3
replies
982
views
How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
gene expression
enrichment
RNA-seq
DESeq2
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
rodrigo.duarte88
▴ 30
2
votes
2
replies
841
views
Limma design matrix separate channel analysis with same control
limma
design matrix
gene expression
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
Guillaume Robert
• 0
1
vote
2
replies
649
views
Microarray Analysis of Sleep Deprivation Data Experimental Design
limma
gene expression
r
diffeential expression
microarray analysis
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
bdighera
• 0
0
votes
5
replies
2.0k
views
Getting opposite log2 fold change
deseq2
gene expression
log2foldchange
R
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
leekun4
• 0
0
votes
3
replies
1.2k
views
How to regress phenotype ~ gene + covars in limma?
limma
gene expression
microarray
R
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
anon20955
• 0
0
votes
2
replies
882
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 4.7 years ago by
James W. MacDonald
65k • written 4.7 years ago by
Guillaume Robert
• 0
0
votes
4
replies
1.1k
views
GOexpress - Error when plotting expression data
RNA-seq
transcriptomics
gene ontology
gene expression
GOexpress
updated 4.3 years ago by
kevin.rue
▴ 350 • written 4.3 years ago by
atorson
• 0
0
votes
3
replies
1.8k
views
Algorithm for between and within microarray normalisation (for meta-analysis).
microarray
meta-analysis
gene expression
updated 5.4 years ago by
Bioconductor Community
0 • written 7.8 years ago by
StephK
▴ 70
2
votes
1
reply
4.8k
views
Using DESeq2 to analyse TCGA data
deseq2
tcga
tcgabiolinks
gene expression
differential expression
updated 6.3 years ago by
Michael Love
42k • written 6.3 years ago by
victor.ramos.usp
• 0
0
votes
2
replies
1.0k
views
Question about Illuminaio
illuminaio
illumina human ht-12 v4
gene expression
micorarray
updated 6.2 years ago by
Mike Smith
★ 6.5k • written 6.2 years ago by
makoouji
• 0
2
votes
4
replies
4.6k
views
WGCNA: intrepreting grey unassigned "module"?
WGCNA
rnaseq
gene expression
co-expression network
updated 6.1 years ago by
Peter Langfelder
★ 3.0k • written 6.1 years ago by
davidjameswheatcroft
▴ 10
3
votes
11
replies
2.4k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression
geoquery
GSE
bioconductor
microarray
updated 5.7 years ago by
Sean Davis
21k • written 5.7 years ago by
mahm
▴ 20
3
votes
4
replies
989
views
edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
edger
rnaseq
gene expression
bioinformatics
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
brett.vanderwerff
• 0
0
votes
0
replies
1.3k
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna
transcriptome
big data
metagenomics
gene expression
6.3 years ago
jol.espinoz
▴ 40
0
votes
0
replies
873
views
Normalisation of Data before loading in TMixClust
rna-seq
tmixclust
k-means clustering
gene expression
genesis
4.4 years ago
astridite
• 0
0
votes
0
replies
1.1k
views
Interpreting Affymetrix Human Genome U133 Plus 2.0 samples
gene expression
gene expression data
cel
affy
affymatrix
6.3 years ago
torgeirous
• 0
0
votes
0
replies
995
views
gene expression data analysis and batch effect methods
batch effect
gene expression
7.0 years ago
tati6406
• 0
0
votes
1
reply
750
views
Obtaining gene expression value for a list of genes
gene expression
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
mahm
▴ 20
1
vote
0
replies
874
views
Job:
Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics
gene expression
time series
plant biology
circadian
Job
4.6 years ago
dezer
▴ 10
0
votes
0
replies
1.1k
views
Bach effect and PEER/RUV correction on large population
methylation
gene expression
sva
batch effect
ruv
7.4 years ago
carleshf
▴ 10
0
votes
0
replies
902
views
Job:
Postdoctoral Research Fellowship- reinforcement learning in biology- London
job
bioinformatician job
machine learning
gene expression
experimental design
Job
5.6 years ago
dezer
▴ 10
0
votes
0
replies
693
views
problem with DeMAND, gene expression matrix input
DeMAND
gene expression
5.5 years ago
chipolino
• 0
39 results • Page
1 of 1
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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