Showing : geneexpression • reset
9
votes
7
replies
9.3k
views
DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 10
5
votes
18
replies
2.9k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
4
votes
2
replies
4.0k
views
Selecting genes based on expressional variance
geneexpression wgcna rnaseq
updated 9.6 years ago by 1.6k • written 9.6 years ago by ▴ 250
3
votes
5
replies
8.6k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 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 ▴ 830 • written 6.5 years ago by • 0
2
votes
3
replies
1.6k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
2
votes
5
replies
1.7k
views
heatmap in R
r language microarray geneexpression
updated 8.7 years ago by ★ 1.0k • written 8.7 years ago by • 0
2
votes
2
replies
410
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
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 ★ 4.1k • written 2.6 years ago by ▴ 10
2
votes
2
replies
1.6k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 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 42k • written 5.6 years ago by ▴ 60
2
votes
2
replies
825
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 2.1 years ago by • 0 • written 2.2 years ago by ▴ 10
2
votes
4
replies
1.7k
views
Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 19 months ago by 42k • written 19 months ago by • 0
2
votes
3
replies
458
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
10 weeks ago jbgnielson • 0
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 42k • written 8.2 years ago by • 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 ★ 28k • written 8.8 years ago by ▴ 10
1
vote
1
reply
5.1k
views
NA p and p adjusted value
geneexpression
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by • 0
1
vote
1
reply
1.2k
views
gene expression data analysis
microarray geneexpression
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
1
vote
3
replies
1.2k
views
General suggestions regarding gene expression
geneexpression
updated 7.2 years ago by 50k • written 7.2 years ago by • 0
1
vote
4
replies
1.8k
views
ddCT Package for StepOnePlus qPCR output
qPCR ddCt geneexpression
updated 6.8 years ago by ▴ 120 • written 6.8 years ago by ▴ 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 21k • written 6.1 years ago by ▴ 10
1
vote
3
replies
968
views
Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
1
vote
1
reply
734
views
Accounting for fish body mass in DE?
GeneExpression edgeR
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
1
vote
3
replies
971
views
DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 3.3 years ago by 42k • written 3.3 years ago by • 0
1
vote
1
reply
775
views
Error while using champ.SVD function
GeneExpression
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
1
vote
0
replies
577
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
22 months ago hlee ▴ 10
0
votes
1
reply
540
views
Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
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 ▴ 830 • written 8.8 years ago by ▴ 10
0
votes
3
replies
1.0k
views
CountOverlap
GeneExpression ChIPSeqData
updated 19 months ago by 65k • written 19 months ago by ▴ 20
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
0
votes
0
replies
443
views
Free Gibbson energy RNA doublex
GeneExpression RNAinteract
21 months ago Tamina • 0
0
votes
1
reply
2.4k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
2
replies
933
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 ★ 1.3k • written 22 months ago by • 0
0
votes
1
reply
480
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 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 ▴ 130 • written 8.0 years ago by ▴ 290
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 20 months ago by • 0 • written 2.0 years ago by • 0
0
votes
1
reply
637
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 23 months ago by 65k • written 23 months ago by • 0
0
votes
0
replies
1.1k
views
Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
9.4 years ago Peter.Wood • 0
0
votes
3
replies
1.6k
views
error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 8.1 years ago by 65k • written 8.1 years ago by ▴ 20
0
votes
0
replies
852
views
Volcano plot: Putting calculated values in legend
GeneExpression
updated 2.1 years ago by ★ 3.9k • written 2.1 years ago by • 0
0
votes
0
replies
1.5k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
10.1 years ago Guest User ★ 13k
0
votes
1
reply
633
views
Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 14 months ago by ★ 4.1k • written 14 months ago by • 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 ★ 3.0k • written 8.5 years ago by • 0
0
votes
0
replies
907
views
Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
7.4 years ago shaheryar • 0
0
votes
2
replies
1.8k
views
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
12 months ago CDSPARKS ▴ 10
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
621
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
3.5 years ago coobzie • 0
0
votes
2
replies
965
views
Gene expression in R
limma edgeR Biobase GeneExpression
2.7 years ago sogol.bouyeh • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Awards • All
Popular Question to Haibo Liu • 0
Popular Question to HS ▴ 10
Popular Question to DevelopingHippo • 0
Scholar to Robert Castelo ★ 3.3k
Popular Question to Gyan Prakash Mishra ▴ 10
Locations • All
United States, just now
United States, 2 minutes ago
United States, 8 minutes ago
United States, 20 minutes ago
United States, 22 minutes ago
Traffic: 654 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6