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RNA-seq
•
reset
41
votes
44
replies
12k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 7.0 years ago by
Wade Davis
▴ 60 • written 7.6 years ago by
yjiangnan
▴ 10
10
votes
14
replies
9.2k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2
rna-seq
8.4 years ago • updated 8.3 years ago
anand_mt
▴ 90
1
vote
14
replies
11k
views
DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq
rna-seq
9.7 years ago
rodriguez.varenka
• 0
1
vote
13
replies
6.7k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2
rna-seq
normalization
8.7 years ago
gil.hornung
• 0
0
votes
13
replies
2.1k
views
Understanding differences in results with and without setting of pairing factor
DESeq2
deseq2
rna-seq
paired samples
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
solgakar@bi.technion.ac.il
▴ 90
1
vote
12
replies
1.6k
views
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq
edger
fitted values
differential expression
normalization
updated 5.5 years ago by
Gordon Smyth
52k • written 5.5 years ago by
David R
▴ 90
18
votes
12
replies
4.1k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR
deseq2
rna-seq
independent filtering
updated 9.5 years ago by
Michael Love
43k • written 9.5 years ago by
Ryan C. Thompson
★ 7.9k
5
votes
12
replies
6.2k
views
DESeq2 time series contrasts between timepoints
rna-seq
deseq2
updated 3.1 years ago by
AZ
▴ 30 • written 7.2 years ago by
gtho123
▴ 40
9
votes
12
replies
8.6k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 7 months ago by
Elizabeth
• 0 • written 9.4 years ago by
gthm
▴ 30
15
votes
12
replies
2.9k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2
ZINB-WaVE
single cell
RNA-seq
differential expression
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
rory.kirchner
▴ 60
3
votes
12
replies
5.6k
views
Batch correction when only some subjects have replicates across batches
limma
batch effect
rna-seq
updated 6.2 years ago by
Peter Langfelder
★ 3.0k • written 6.2 years ago by
Mike A
▴ 10
4
votes
11
replies
2.6k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps
summarizedexperiment
count matrix
low counts
rna-seq
updated 8.8 years ago by
Valerie Obenchain
★ 6.8k • written 8.8 years ago by
shania90.lk
▴ 10
24
votes
11
replies
19k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom
limma
voom
rna-seq
quantile normalization
updated 8.9 years ago by
Gordon Smyth
52k • written 8.9 years ago by
lassancejm
▴ 50
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport
Kallisto
rna-seq
updated 7.8 years ago by
pablo_garcia05
▴ 20 • written 8.7 years ago by
cguzman.bioinformatics
▴ 10
0
votes
11
replies
1.8k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
5.7 years ago
saddamhusain77
• 0
2
votes
11
replies
3.5k
views
Cannot find header.json in salmon index directory
salmon
tximeta
rna-seq
5.1 years ago • updated 5.0 years ago
mico
• 0
5
votes
11
replies
3.8k
views
DESeq2 logfoldchange and interaction in model
deseq2
R
logfoldchange
rna-seq
5.5 years ago • updated 5.4 years ago
pierre.marin
• 0
3
votes
11
replies
2.2k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq
scRNA-seq
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Bogdan
▴ 670
2
votes
10
replies
2.1k
views
Coseq error with DESeq2 object: Error in "normFactors"
coseq
rna-seq
updated 5.8 years ago by
andrea.rau
▴ 80 • written 5.8 years ago by
varunorama
• 0
0
votes
10
replies
2.7k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.7 years ago by
saddamhusain77
• 0
12
votes
10
replies
7.8k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.7 years ago • updated 5.9 years ago
rached
▴ 60
2
votes
10
replies
11k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
fromhj304
▴ 10
2
votes
10
replies
2.3k
views
Design matrix for unbalanced data
edgeR
RNA-Seq
design matrix
multifactorial design
8.8 years ago
Yogender Gowtham
▴ 20
2
votes
9
replies
2.4k
views
i can't find cummeRbund package
software error
cuumeRbund
rna-seq
updated 9.3 years ago by
Martin Morgan
25k • written 9.3 years ago by
Angel
▴ 40
1
vote
9
replies
2.3k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs
RNA-Seq
Isoforms
DTU
expression
updated 5.4 years ago by
fruce_ki
▴ 20 • written 5.4 years ago by
UserAnonyme
• 0
14
votes
9
replies
16k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
9.9 years ago
gavrielmatt
▴ 30
5
votes
9
replies
2.3k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
2.4 years ago
Yang Shi
▴ 10
3
votes
9
replies
2.7k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq
tximeta
4.0 years ago
Pufall, Miles A
▴ 30
10
votes
9
replies
2.0k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom
voom
limma
rna-seq
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
vd4mmind
• 0
4
votes
9
replies
1.7k
views
RNA-seq analysis edgeR
rna-seq
edger
updated 8.1 years ago by
Ryan C. Thompson
★ 7.9k • written 8.1 years ago by
es874
▴ 20
14
votes
9
replies
4.2k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma
rna-seq
removebatcheffect()
updated 6.9 years ago by
alakatos
▴ 130 • written 8.6 years ago by
Ekarl2
▴ 80
2
votes
8
replies
2.0k
views
Transcript variant analysis on Salmon output
Salmon
RNA-Seq
Transcript variant analysis
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
saddamhusain77
• 0
1
vote
8
replies
3.4k
views
RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq
edgeR
estimatedispersions
bacteria
9.9 years ago • updated 9.8 years ago
Mauve
• 0
11
votes
8
replies
9.8k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA
RNA-Seq
DESeq2
voom
removebatcheffect()
updated 8.2 years ago by
Peter Langfelder
★ 3.0k • written 8.2 years ago by
gokce.ouz
▴ 70
4
votes
8
replies
24k
views
Variance stabilising transformation for machine learning
deseq2
vst
rna-seq
machine-learning
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
Manik Garg
▴ 20
1
vote
8
replies
2.1k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq
time series
patient
limma-voom
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
aec
▴ 90
0
votes
8
replies
2.6k
views
Isoforms detection using bioconductor
bioconductor
biomart
granges
rna-seq
updated 7.4 years ago by
Michael Lawrence
★ 11k • written 7.4 years ago by
seungjoon.kim
• 0
0
votes
8
replies
2.4k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq
deseq2
deseq
R
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
arun.thirumaran
• 0
4
votes
8
replies
1.5k
views
problem in designing matrix and batch effect
edger
rna-seq
matrix
updated 4.9 years ago by
James W. MacDonald
67k • written 4.9 years ago by
alihakimzadeh73
• 0
3
votes
8
replies
3.9k
views
Normalisation in DESeq2
deseq2
rna-seq
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
thjnant
▴ 10
1
vote
8
replies
8.9k
views
DESeq2: Continuous and discreate variables in the design
deseq2
R
rna-seq
design
updated 4.0 years ago by
Michael Love
43k • written 5.0 years ago by
raquelgarza95
• 0
4
votes
8
replies
2.7k
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
updated 22 months ago by
James W. MacDonald
67k • written 4.5 years ago by
morteza.aslanzadeh
▴ 30
0
votes
7
replies
2.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 3.1 years ago by
nicolette.sipperly
• 0 • written 7.6 years ago by
urjaswita
▴ 40
2
votes
7
replies
2.3k
views
RNA-seq with Salmon and tximport
RNA-seq
Salmon
tximport
updated 5.3 years ago by
James W. MacDonald
67k • written 5.3 years ago by
woojoy14
• 0
8
votes
7
replies
6.2k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma
duplicateCorrelation
rna-seq
technical replicates
biological replicates
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
paul.alto
▴ 50
3
votes
7
replies
6.0k
views
What does this error mean? - issue implementing SVA
sva
rna-seq
updated 6.7 years ago by
Sandip Darji
▴ 30 • written 8.8 years ago by
kmuench
▴ 40
6
votes
7
replies
4.5k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq
rna-seq
linear model
limma
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
Thomas Sandmann
▴ 90
5
votes
7
replies
4.0k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
thindmarsmission
▴ 10
3
votes
7
replies
2.1k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2
twins
design
formula
RNA-seq
7.1 years ago
Simone
• 0
5
votes
7
replies
2.7k
views
limma - blocking or regressing out nuisance variable
limma
voom
RNA-seq
updated 5.6 years ago by
James W. MacDonald
67k • written 5.6 years ago by
biomiha
▴ 20
50 results • Page
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Comment: Cannot install GO.db and org.Hs.eg.db
by
Gabriel
• 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
by
Michael Love
43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts
by
Gordon Smyth
52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Answer: Feature Counts -R XS Read Assignment Tag
by
Gordon Smyth
52k
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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