Showing : rnaseqdata • reset
0
votes
0
replies
628
views
Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData RNASeq
3.4 years ago Pang • 0
0
votes
1
reply
1.1k
views
I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
1
vote
7
replies
2.9k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
2
votes
9
replies
4.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.5 years ago Peipei • 0
1
vote
5
replies
1.9k
views
Error in DEseq
DEseq RNASeqData
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
1
vote
1
reply
1.2k
views
NOIseq Probability column
RNAseq RNASeqData NOISeq
3.6 years ago • updated 3.5 years ago Pratibha ▴ 10
5
votes
4
replies
2.7k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 10 months ago by • 0 • written 3.6 years ago by ▴ 30
0
votes
2
replies
2.4k
views
How to run vst transformation
RNASeqData vst
updated 3.6 years ago by 43k • written 3.7 years ago by • 0
2
votes
3
replies
1.9k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3.7 years ago Maka • 0
0
votes
5
replies
3.4k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
3.7 years ago • updated 3.6 years ago priyanka.m • 0
22
votes
15
replies
12k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 2.1 years ago by ▴ 10 • written 3.7 years ago by ▴ 50
0
votes
2
replies
1.6k
views
Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
3
votes
2
replies
1.8k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.7 years ago Dakarai ▴ 10
0
votes
1
reply
1.2k
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
2
replies
2.1k
views
lncRNA Genes in a Dataset
ncRNAtools RNASeqData
3.8 years ago • updated 3.7 years ago sushimoto • 0
0
votes
0
replies
870
views
edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
3.8 years ago Mafalda • 0
1
vote
4
replies
1.6k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
3.8 years ago sushimoto • 0
0
votes
0
replies
1.1k
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
3.8 years ago treebig44 ▴ 40
0
votes
0
replies
1.3k
views
high number of reads mapped to too many loci
RNASeqData
3.8 years ago vasa.broz • 0
0
votes
1
reply
1.2k
views
HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
3.8 years ago karl.stamm ▴ 10
4
votes
1
reply
3.8k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 40
1
vote
1
reply
1.0k
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 40
4
votes
6
replies
13k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.8 years ago treebig44 ▴ 40
1
vote
1
reply
4.1k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
1
vote
2
replies
1.4k
views
Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
3.8 years ago m.glymenaki • 0
1
vote
1
reply
1.2k
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
4
votes
3
replies
1.9k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 3.9 years ago by ★ 1.4k • written 3.9 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.9 years ago Raito92 ▴ 60
0
votes
1
reply
2.1k
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
3.9 years ago bas_work ▴ 30
1
vote
1
reply
2.2k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
2
votes
4
replies
1.9k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
4.3 years ago khaveh ▴ 10
0
votes
2
replies
1.2k
views
Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
4.4 years ago szomolay • 0
0
votes
1
reply
1.1k
views
Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 4.6 years ago by ▴ 760 • written 4.6 years ago by • 0
0
votes
3
replies
1.5k
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 4.6 years ago by ★ 1.4k • written 4.6 years ago by • 0
0
votes
1
reply
1.3k
views
t.fit stops in masigpro while running RNA seq data
RNASeqData maSigPro
4.7 years ago subashika • 0
8
votes
2
replies
10k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
4.7 years ago paty ▴ 60
1
vote
3
replies
3.3k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
4.7 years ago dantasezequiel1 • 0
1
vote
15
replies
3.9k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
4.7 years ago demisa • 0
0
votes
6
replies
1.8k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
4.7 years ago Rishav ▴ 20
2
votes
8
replies
4.0k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 4.7 years ago by 53k • written 4.7 years ago by ▴ 20
3
votes
4
replies
2.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
4.7 years ago hgalmoore • 0
7
votes
4
replies
17k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 4.0 years ago by • 0 • written 4.8 years ago by ▴ 20
3
votes
2
replies
1.4k
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
4.8 years ago Wuschel ▴ 10
1
vote
6
replies
2.1k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
4.9 years ago Seaweed • 0
9
votes
5
replies
5.3k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
5.1 years ago ecg1g15 ▴ 30
3
votes
6
replies
1.9k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 50
2
votes
4
replies
3.7k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
5.1 years ago ecg1g15 ▴ 30
0
votes
1
reply
916
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
0
votes
3
replies
9.5k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
0
votes
1
reply
1.3k
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 80
152 results • Page 3 of 4
Recent ...
Replies
Comment: Empty boxes in treemap plot rrvgo package by TikTsokaasocissalpc • 0
Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
Comment: nice 3D displays for PCA analysis by adam80haynes • 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital by TikTsokaasocissalpc • 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes by TikTsokaasocissalpc • 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers by Gordon Smyth 53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Votes
Error in SummarizedExperiment(assays = SimpleList(counts = countData)
Answer: DESeq2 class error: superclass "ExpData" not defined in the environment of the o
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Hervé Pagès 16k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Istvan Albert ▴ 50
Popular Question to Dario Strbenac ★ 1.6k
Locations • All
United States, 3 minutes ago
United States, 14 minutes ago
The city by the bay, 52 minutes ago
United States, 1 hour ago
Barcelona, Spain, 3 hours ago
Traffic: 1330 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