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GeneExpression
•
reset
2
votes
3
replies
452
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
9 weeks ago
jbgnielson
• 0
2
votes
2
replies
406
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
5 months ago
Manthos
• 0
2
votes
3
replies
1.6k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
gingergeiger22
• 0
0
votes
1
reply
476
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression
Bioconductor
GEOquery
MethylationArrayData
9 months ago
Arianna
• 0
0
votes
2
replies
1.7k
views
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
12 months ago
CDSPARKS
▴ 10
0
votes
1
reply
629
views
Heatmap of two conditions from the normalized gene count data
GeneExpression
heatmaps
updated 14 months ago by
ATpoint
★ 4.1k • written 14 months ago by
Amazing570
• 0
0
votes
1
reply
2.4k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 14 months ago by
ATpoint
★ 4.1k • written 14 months ago by
bio.boi
• 0
2
votes
4
replies
1.7k
views
Comparing different method for DESEQ2
DESeq2
GeneExpression
updated 19 months ago by
Michael Love
41k • written 19 months ago by
Vapin
• 0
0
votes
3
replies
997
views
CountOverlap
GeneExpression
ChIPSeqData
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
michela
▴ 20
0
votes
0
replies
442
views
Free Gibbson energy RNA doublex
GeneExpression
RNAinteract
20 months ago
Tamina
• 0
1
vote
0
replies
572
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
22 months ago
hlee
▴ 10
0
votes
2
replies
931
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression
GeneExpression
R
enrichment
DEGseq
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
ac.mainul.mmb
• 0
0
votes
1
reply
538
views
Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 22 months ago by
Basti
▴ 780 • written 22 months ago by
Iraide
• 0
0
votes
1
reply
634
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression
NanoporeRNASeq
DESeq2
GeneExpression
DEVis
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
Ana
• 0
1
vote
1
reply
769
views
Error while using champ.SVD function
GeneExpression
updated 2.0 years ago by
Basti
▴ 780 • written 2.0 years ago by
Afrin
• 0
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 19 months ago by
Aurora
• 0 • written 2.0 years ago by
mahsa
• 0
0
votes
0
replies
846
views
Volcano plot: Putting calculated values in legend
GeneExpression
updated 2.1 years ago by
Kevin Blighe
★ 3.9k • written 2.1 years ago by
Narender Singh
• 0
2
votes
2
replies
820
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression
DESeq2
ExpressionData
updated 2.1 years ago by
fivescarynightsgames
• 0 • written 2.2 years ago by
reza
▴ 10
0
votes
2
replies
2.0k
views
Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression
GeneExpression
DESeq2
Design()
2.6 years ago
p.l.chen
• 0
2
votes
2
replies
6.8k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression
GeneExpression
DESeq2
R
updated 2.6 years ago by
ATpoint
★ 4.1k • written 2.6 years ago by
janjoy
▴ 10
0
votes
2
replies
961
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
2.7 years ago • updated 2.6 years ago
sogol.bouyeh
• 0
2
votes
2
replies
1.6k
views
DESeq2 - one groups with no replicates
DESeq2
rnaseqGene
DifferentialExpression
GeneExpression
2.9 years ago
SUMIT
• 0
5
votes
18
replies
2.9k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow
DESeq2
GeneExpression
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
Yosapol
• 0
1
vote
3
replies
966
views
DESeq analysis with Biological replicate.
DESeq2
ExpressionData
GeneExpression
updated 3.3 years ago by
Michael Love
41k • written 3.3 years ago by
Javad_Sadeghi
• 0
1
vote
1
reply
732
views
Accounting for fish body mass in DE?
GeneExpression
edgeR
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
michael.lawrence
• 0
0
votes
1
reply
747
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 3.4 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 3.4 years ago by
Will
• 0
1
vote
3
replies
967
views
Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression
R
limma
MultipleComparison
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
Gwénolé
• 0
0
votes
0
replies
619
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression
methyAnalysis
MethylationArray
3.5 years ago
coobzie
• 0
2
votes
5
replies
11k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2
r
fpkm()
geneexpression
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
Beginner
▴ 60
1
vote
4
replies
2.0k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress
geoquery
geneexpression
updated 6.1 years ago by
Sean Davis
21k • written 6.1 years ago by
arbet003
▴ 10
3
votes
1
reply
1.7k
views
Processing several GSM from GEO database using Barcode and fRMA
frma
barcode
geneexpression
gsm
ncbi geo
updated 6.5 years ago by
Matthew McCall
▴ 830 • written 6.5 years ago by
diana.elassal
• 0
1
vote
4
replies
1.8k
views
ddCT Package for StepOnePlus qPCR output
qPCR
ddCt
geneexpression
updated 6.8 years ago by
Zhang, Jitao David
▴ 120 • written 6.8 years ago by
rbronste
▴ 60
1
vote
3
replies
1.2k
views
General suggestions regarding gene expression
geneexpression
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
mariagiovannetti86
• 0
0
votes
0
replies
900
views
Where or how to find the gene interaction with itself?
microarray
gene interaction
geneexpression
7.4 years ago
shaheryar
• 0
0
votes
0
replies
1.2k
views
Error in SAMseq analysis with R
r
samseq
microarray
rnaseq
geneexpression
7.7 years ago
namilio
• 0
0
votes
0
replies
1.2k
views
Methylation and gene expression
methylation
geneexpression
7.7 years ago
Asma rabe
▴ 290
0
votes
2
replies
1.1k
views
Methylation and gene expression data
methylation
geneexpression
updated 8.0 years ago by
arfranco
▴ 130 • written 8.0 years ago by
Asma rabe
▴ 290
0
votes
3
replies
1.6k
views
error in drawing MDS plot for eset
MDSplot
geneexpression
insilicomerging
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
Shamim Sarhadi
▴ 20
1
vote
6
replies
1.8k
views
how to deal the effect of enormous gene expression?
deseq2
rnaseq
tomato
geneexpression
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
hamaor
• 0
0
votes
1
reply
1.3k
views
Error in MetaQC R package.
r
metaqc
microarray
geneexpression
8.4 years ago
Agaz Hussain Wani
▴ 260
0
votes
3
replies
1.8k
views
problem with WGCNA
geneexpression
updated 8.5 years ago by
Peter Langfelder
★ 3.0k • written 8.5 years ago by
nazaninhoseinkhan
• 0
2
votes
5
replies
1.7k
views
heatmap in R
r language
microarray
geneexpression
updated 8.7 years ago by
Axel Klenk
★ 1.0k • written 8.7 years ago by
ifaizurahredzuan
• 0
1
vote
1
reply
1.2k
views
gene expression data analysis
microarray
geneexpression
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
ifaizurahredzuan
• 0
1
vote
1
reply
5.1k
views
NA p and p adjusted value
geneexpression
updated 8.7 years ago by
Peter Langfelder
★ 3.0k • written 8.7 years ago by
timarogger
• 0
1
vote
2
replies
5.7k
views
explanation of makeContrasts function of limma package
limma
microarray
R
geneexpression
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
elisa.micarelli
▴ 10
0
votes
3
replies
11k
views
How to combine expression values of multiple probes for one gene
probe
convert
geneexpression
onechannelgui
updated 8.8 years ago by
svlachavas
▴ 830 • written 8.8 years ago by
ayanava18
▴ 10
0
votes
0
replies
1.1k
views
Using segAnglePo() for a set of genes
geneexpression
genesetenrichment
segAnglePo
9.4 years ago
Peter.Wood
• 0
3
votes
5
replies
8.5k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
Peter Crisp
▴ 10
9
votes
7
replies
9.3k
views
DESeq2 timecourse - How to set the experimental design
deseq2
geneexpression
timecourse
updated 9.6 years ago by
Wolfgang Huber
★ 13k • written 9.6 years ago by
nafeesa
▴ 10
4
votes
2
replies
4.0k
views
Selecting genes based on expressional variance
geneexpression
wgcna
rnaseq
updated 9.6 years ago by
Laurent Gatto
1.6k • written 9.6 years ago by
Jon Bråte
▴ 250
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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