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rnaseqdata
•
reset
1
vote
3
replies
1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
3.0 years ago
dantasezequiel1
• 0
2
votes
3
replies
1.3k
views
RNA-seq analysis without replicates
DESeq2
RESEQ
RNASeqData
updated 12 months ago by
Cynthia
• 0 • written 12 months ago by
4214811
• 0
0
votes
2
replies
631
views
Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma
RNASeqData
edgeR
updated 13 months ago by
Hilary
▴ 30 • written 13 months ago by
Lucas
• 0
1
vote
7
replies
791
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 4 months ago by
Gordon Smyth
50k • written 6 months ago by
Gimena
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 11 months ago by
informatician
• 0
1
vote
2
replies
2.5k
views
Understanding how to contrast two treatments in DESeq2
DESeq2
RNASeqData
updated 19 months ago by
swbarnes2
★ 1.3k • written 19 months ago by
Jennifer M
• 0
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2
RNASeqData
DifferentialExpression
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
Ben
▴ 50
0
votes
10
replies
2.8k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer
RNAseqData
GenomicFeatures
Cancer
RNAseqData
GenomicFeatures
updated 9.8 years ago by
Fong Chun Chan
▴ 320 • written 9.8 years ago by
Valerie Obenchain
★ 6.8k
0
votes
1
reply
317
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 4 months ago by
Michael Love
41k • written 5 months ago by
Pez
▴ 10
0
votes
1
reply
622
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
khaserdene99
• 0
0
votes
1
reply
1.0k
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2
multiple factor design
rnaseqdata
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
Dimitris Polychronopoulos
▴ 80
0
votes
5
replies
2.1k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData
isoform
DESeq2
2.0 years ago • updated 23 months ago
priyanka.m
• 0
6
votes
4
replies
10k
views
How to use combat in order to remove batch effects?
BatchEffect
DESeq2
RNASeqData
updated 2.3 years ago by
BioNovice247
• 0 • written 3.1 years ago by
Emma
▴ 10
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.0 years ago
hgalmoore
• 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 13 months ago by
Rebekah
• 0
4
votes
1
reply
2.3k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2
RNASeq
RNASeqData
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
treebig44
▴ 30
0
votes
1
reply
544
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData
DESeq2
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Abhishek Singh
▴ 20
0
votes
3
replies
724
views
Understanding edgeR differential expression results
Transcriptomics
edgeR
DifferentialExpression
RNASeqData
RNASeq
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Teresa
• 0
0
votes
2
replies
1.3k
views
How to run vst transformation
RNASeqData
vst
updated 23 months ago by
Michael Love
41k • written 23 months ago by
sropri
• 0
2
votes
4
replies
2.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova
RNASeqData
tukeyTest
DESeq2
3.4 years ago
ecg1g15
▴ 20
0
votes
6
replies
748
views
Questionable limma results for differential expression on RNA-seq
RNASeqData
DifferentialExpression
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gld-bioinf
• 0
0
votes
2
replies
614
views
RNA-Seq and disease outcome analysis
rnaseqAnalysis
RNASeqData
13 months ago
JonasEnder
• 0
3
votes
2
replies
915
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData
DEGreport
edgeR
3.1 years ago
Wuschel
▴ 10
22
votes
15
replies
7.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 5 months ago by
Marie
▴ 10 • written 2.0 years ago by
Dina
▴ 50
1
vote
1
reply
632
views
Strange error while running DESeq() function.
DESeq2
RNASeq
RNASeqData
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
treebig44
▴ 30
4
votes
3
replies
1.2k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2
idep
RNASeqData
updated 2.2 years ago by
swbarnes2
★ 1.3k • written 2.2 years ago by
student2
▴ 10
0
votes
2
replies
316
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
4 months ago
Luca
• 0
0
votes
1
reply
549
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2
RNASeqData
DifferentialExpression
updated 15 months ago by
ATpoint
★ 4.0k • written 15 months ago by
Julie
• 0
1
vote
1
reply
568
views
DESEQ2 differential expression for subsets of data?
RNASeqData
DESeq2
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
amnahsiddiqa
▴ 10
1
vote
1
reply
390
views
Deseq contrast question
RNASeqData
DESeq2
updated 10 months ago by
Michael Love
41k • written 10 months ago by
Hannah
▴ 10
1
vote
2
replies
1.5k
views
Binning expression data along with capturing gene identifiers
rnaseqdata
clustering
updated 9.2 years ago by
Johannes Rainer
★ 2.0k • written 9.2 years ago by
Alan Smith
▴ 150
0
votes
2
replies
760
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR
DEGs
DESEQ2
RNASeqData
2.2 years ago
Raito92
▴ 60
2
votes
8
replies
2.3k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Rishav
▴ 20
0
votes
2
replies
1.1k
views
lncRNA Genes in a Dataset
ncRNAtools
RNASeqData
2.0 years ago
sushimoto
• 0
1
vote
2
replies
500
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData
DESeq2
updated 8 months ago by
Michael Love
41k • written 9 months ago by
mohammad.hossein.banabazi
• 0
1
vote
4
replies
1.0k
views
lncRNA Differential Expression Analysis
DESeq2
limma
RNASeqData
2.1 years ago • updated 2.0 years ago
sushimoto
• 0
0
votes
4
replies
628
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
sohail.mbio
▴ 10
0
votes
6
replies
1.2k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.0 years ago
Rishav
▴ 20
2
votes
9
replies
2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
22 months ago
Peipei
• 0
1
vote
4
replies
1.2k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2
Log2FC
RNASeqData
15 months ago
Iwan
• 0
3
votes
3
replies
1.3k
views
How to formulate 2 factor nested design in DESeq2
nested_design
RNASeqData
DESeq2
22 months ago
JK Kim
▴ 20
0
votes
1
reply
620
views
HSMMSingleCell metadata
ExperimentHubData
ExpressionData
CellDataSet
RNASeqData
2.1 years ago
karl.stamm
▴ 10
1
vote
6
replies
1.3k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData
DESeq2
rnaseqGene
3.2 years ago
Seaweed
• 0
1
vote
1
reply
1.1k
views
Help understanding edgeR code for doing exactTest
exacttest
RNASeqData
edgeR
diffGeneAnalysis
updated 2.5 years ago by
Gordon Smyth
50k • written 2.5 years ago by
Julia
• 0
1
vote
1
reply
307
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
kaurprab
• 0
1
vote
2
replies
648
views
Installation of R-packages for RNA-seq analysis
RNASeqData
14 months ago
Begin-R
• 0
0
votes
3
replies
655
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
4 months ago
Oenone
• 0
8
votes
2
replies
6.7k
views
handling outliers with DESeq2
RNASeqData
DESeq2
Outliers
3.0 years ago
paty
▴ 60
2
votes
4
replies
1.2k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData
DESeq2
2.6 years ago
khaveh
▴ 10
7
votes
5
replies
3.3k
views
Normalise to a housekeeping gene in DESEq2
DESeq2
housekeeping
R
RNASeqData
3.4 years ago
ecg1g15
▴ 20
50 results • Page
1 of 1
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Replies
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark
by
jacques.imbert
• 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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