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Showing :
geneexpression
•
reset
2
votes
3
replies
377
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
29 days ago • updated 28 days ago
jbgnielson
• 0
2
votes
2
replies
354
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
4 months ago
Manthos
• 0
2
votes
3
replies
1.3k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
gingergeiger22
• 0
0
votes
1
reply
405
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression
Bioconductor
GEOquery
MethylationArrayData
8 months ago
Arianna
• 0
0
votes
2
replies
1.5k
views
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
11 months ago
CDSPARKS
▴ 10
0
votes
1
reply
565
views
Heatmap of two conditions from the normalized gene count data
GeneExpression
heatmaps
updated 12 months ago by
ATpoint
★ 4.0k • written 13 months ago by
Amazing570
• 0
0
votes
1
reply
2.1k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
bio.boi
• 0
2
votes
4
replies
1.6k
views
Comparing different method for DESEQ2
DESeq2
GeneExpression
updated 18 months ago by
Michael Love
41k • written 18 months ago by
Vapin
• 0
0
votes
3
replies
922
views
CountOverlap
GeneExpression
ChIPSeqData
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
michela
▴ 20
0
votes
0
replies
416
views
Free Gibbson energy RNA doublex
GeneExpression
RNAinteract
19 months ago
Tamina
• 0
1
vote
0
replies
518
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
20 months ago
hlee
▴ 10
0
votes
2
replies
889
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 21 months ago by
swbarnes2
★ 1.3k • written 21 months ago by
ac.mainul.mmb
• 0
0
votes
1
reply
503
views
Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 21 months ago by
Basti
▴ 750 • written 21 months ago by
Iraide
• 0
0
votes
1
reply
603
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression
NanoporeRNASeq
DESeq2
GeneExpression
DEVis
updated 22 months ago by
James W. MacDonald
65k • written 22 months ago by
Ana
• 0
1
vote
1
reply
721
views
Error while using champ.SVD function
GeneExpression
updated 23 months ago by
Basti
▴ 750 • written 23 months ago by
Afrin
• 0
0
votes
1
reply
1.8k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 18 months ago by
Aurora
• 0 • written 23 months ago by
mahsa
• 0
0
votes
0
replies
807
views
Volcano plot: Putting calculated values in legend
GeneExpression
updated 23 months ago by
Kevin Blighe
★ 3.9k • written 23 months ago by
Narender Singh
• 0
2
votes
2
replies
781
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression
DESeq2
ExpressionData
updated 2.0 years ago by
fivescarynightsgames
• 0 • written 2.1 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()
2.5 years ago
p.l.chen
• 0
2
votes
2
replies
6.6k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression
GeneExpression
DESeq2
R
updated 2.5 years ago by
ATpoint
★ 4.0k • written 2.5 years ago by
janjoy
▴ 10
0
votes
2
replies
906
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
2.6 years ago • updated 2.5 years ago
sogol.bouyeh
• 0
2
votes
2
replies
1.6k
views
DESeq2 - one groups with no replicates
DESeq2
rnaseqGene
DifferentialExpression
GeneExpression
2.8 years ago
SUMIT
• 0
5
votes
18
replies
2.7k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow
DESeq2
GeneExpression
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
Yosapol
• 0
1
vote
3
replies
920
views
DESeq analysis with Biological replicate.
DESeq2
ExpressionData
GeneExpression
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
Javad_Sadeghi
• 0
1
vote
1
reply
693
views
Accounting for fish body mass in DE?
GeneExpression
edgeR
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
michael.lawrence
• 0
0
votes
1
reply
725
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 3.3 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.3 years ago by
Will
• 0
1
vote
3
replies
924
views
Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression
R
limma
MultipleComparison
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
Gwénolé
• 0
0
votes
0
replies
597
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression
methyAnalysis
MethylationArray
3.4 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 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
Beginner
▴ 60
1
vote
4
replies
1.9k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress
geoquery
geneexpression
updated 6.0 years ago by
Sean Davis
21k • written 6.0 years ago by
arbet003
▴ 10
3
votes
1
reply
1.6k
views
Processing several GSM from GEO database using Barcode and fRMA
frma
barcode
geneexpression
gsm
ncbi geo
updated 6.4 years ago by
Matthew McCall
▴ 830 • written 6.4 years ago by
diana.elassal
• 0
1
vote
4
replies
1.8k
views
ddCT Package for StepOnePlus qPCR output
qPCR
ddCt
geneexpression
updated 6.7 years ago by
Zhang, Jitao David
▴ 120 • written 6.7 years ago by
rbronste
▴ 60
1
vote
3
replies
1.2k
views
General suggestions regarding gene expression
geneexpression
updated 7.1 years ago by
Gordon Smyth
50k • written 7.1 years ago by
mariagiovannetti86
• 0
0
votes
0
replies
872
views
Where or how to find the gene interaction with itself?
microarray
gene interaction
geneexpression
7.3 years ago
shaheryar
• 0
0
votes
0
replies
1.1k
views
Error in SAMseq analysis with R
r
samseq
microarray
rnaseq
geneexpression
7.6 years ago
namilio
• 0
0
votes
0
replies
1.1k
views
Methylation and gene expression
methylation
geneexpression
7.6 years ago
Asma rabe
▴ 290
0
votes
2
replies
1.1k
views
Methylation and gene expression data
methylation
geneexpression
updated 7.9 years ago by
arfranco
▴ 130 • written 7.9 years ago by
Asma rabe
▴ 290
0
votes
3
replies
1.6k
views
error in drawing MDS plot for eset
MDSplot
geneexpression
insilicomerging
updated 8.0 years ago by
James W. MacDonald
65k • written 8.0 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 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
hamaor
• 0
0
votes
1
reply
1.3k
views
Error in MetaQC R package.
r
metaqc
microarray
geneexpression
8.3 years ago
Agaz Hussain Wani
▴ 260
0
votes
3
replies
1.7k
views
problem with WGCNA
geneexpression
updated 8.4 years ago by
Peter Langfelder
★ 2.9k • written 8.4 years ago by
nazaninhoseinkhan
• 0
2
votes
5
replies
1.6k
views
heatmap in R
r language
microarray
geneexpression
updated 8.6 years ago by
Axel Klenk
▴ 990 • written 8.6 years ago by
ifaizurahredzuan
• 0
1
vote
1
reply
1.1k
views
gene expression data analysis
microarray
geneexpression
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
ifaizurahredzuan
• 0
1
vote
1
reply
5.1k
views
NA p and p adjusted value
geneexpression
updated 8.6 years ago by
Peter Langfelder
★ 2.9k • written 8.6 years ago by
timarogger
• 0
1
vote
2
replies
5.6k
views
explanation of makeContrasts function of limma package
limma
microarray
R
geneexpression
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 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 8.7 years ago by
svlachavas
▴ 830 • written 8.7 years ago by
ayanava18
▴ 10
0
votes
0
replies
1.1k
views
Using segAnglePo() for a set of genes
geneexpression
genesetenrichment
segAnglePo
9.3 years ago
Peter.Wood
• 0
3
votes
5
replies
8.4k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 9.4 years ago by
Steve Lianoglou
★ 13k • written 9.4 years ago by
Peter Crisp
▴ 10
9
votes
7
replies
9.2k
views
DESeq2 timecourse - How to set the experimental design
deseq2
geneexpression
timecourse
updated 9.5 years ago by
Wolfgang Huber
★ 13k • written 9.5 years ago by
nafeesa
▴ 10
4
votes
2
replies
4.0k
views
Selecting genes based on expressional variance
geneexpression
wgcna
rnaseq
updated 9.5 years ago by
Laurent Gatto
1.6k • written 9.5 years ago by
Jon Bråte
▴ 250
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
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DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
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