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Showing :
GeneExpression
•
reset
2
votes
3
replies
449
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
403
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
474
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
626
views
Heatmap of two conditions from the normalized gene count data
GeneExpression
heatmaps
updated 13 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
441
views
Free Gibbson energy RNA doublex
GeneExpression
RNAinteract
20 months ago
Tamina
• 0
1
vote
0
replies
571
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
928
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
633
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
765
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
843
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
817
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
957
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
965
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
731
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
746
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
966
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
618
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
898
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
1.2k
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
50 results • Page
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Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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