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Showing :
geneexpression
•
reset
2
votes
3
replies
389
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
4 weeks ago • updated 29 days ago
jbgnielson
• 0
2
votes
2
replies
356
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
409
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
570
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
924
views
CountOverlap
GeneExpression
ChIPSeqData
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
michela
▴ 20
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
417
views
Free Gibbson energy RNA doublex
GeneExpression
RNAinteract
19 months ago
Tamina
• 0
1
vote
0
replies
519
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
891
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
507
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
605
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
722
views
Error while using champ.SVD function
GeneExpression
updated 23 months ago by
Basti
▴ 750 • written 23 months ago by
Afrin
• 0
0
votes
0
replies
809
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
783
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
910
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
923
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
696
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
727
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
927
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
600
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
875
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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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
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Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
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Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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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…
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transcript name mapping between human and mouse
transcript name mapping between human and mouse
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Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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