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Votes
3
votes
3
replies
2.6k
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
2.5 years ago
amnahsiddiqa
▴ 10
0
votes
2
replies
2.0k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR
SingleCellExperiment
SingleCellData
2.5 years ago
Matvii Mykhailichenko
• 0
0
votes
3
replies
1.5k
views
DECIPHER IdTaxa: Speed up training?
DECIPHER
idtaxa
updated 2.5 years ago by
Erik Wright
▴ 150 • written 2.5 years ago by
Till
▴ 30
0
votes
5
replies
1.9k
views
DESeq2 design formula
designformula
DESeq2
updated 2.5 years ago by
swbarnes2
★ 1.4k • written 2.5 years ago by
Grace.Ciabattoni
• 0
0
votes
1
reply
1.2k
views
really low padj value from DESeq2
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
Sara
• 0
2
votes
3
replies
2.6k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
886
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
2.5 years ago
amnahsiddiqa
▴ 10
0
votes
1
reply
990
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 2.5 years ago by
António Miguel de Jesus Domingues
▴ 510
1
vote
1
reply
1.0k
views
DESEQ2 differential expression for subsets of data?
RNASeqData
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
amnahsiddiqa
▴ 10
4
votes
6
replies
2.1k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
2.5 years ago
abhisek001
• 0
0
votes
2
replies
927
views
plotCounts label each sample
p
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
claire
• 0
0
votes
2
replies
1.3k
views
Heat Map
ColData
pheatmap
DESeq2
written 2.5 years ago by
dania.khalid
• 0
1
vote
6
replies
3.3k
views
Choosing between VST and rlog for PCA for outlier identification in DESeq2 when small number of samples
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
nisreen.khambati
• 0
0
votes
0
replies
723
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount
csaw
paired
2.5 years ago
julie.chevalier
• 0
0
votes
2
replies
1.9k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
2.5 years ago
gernophil
• 0
1
vote
1
reply
1.2k
views
IsoformSwitchAnalyzeR Error in reading GTF file
IsoformSwitchAnalyzeR
2.5 years ago
venura
• 0
0
votes
2
replies
866
views
Visualization of absolute values after batch effect correction
limma
updated 2.5 years ago by
SamGG
▴ 360 • written 2.5 years ago by
mobin
• 0
0
votes
1
reply
2.5k
views
How to make OPLS-DA variable importance plot
crlmm
ropls
Metabolomics
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Charlotte
• 0
0
votes
1
reply
1.1k
views
DiffBind output issues
DiffBind
updated 2.5 years ago by
Rory Stark
★ 5.2k • written 2.5 years ago by
David.Atkinson2
• 0
1
vote
2
replies
1.5k
views
Interpret plots from DiffBind
DiffBind
2.5 years ago
Chris
▴ 20
2
votes
3
replies
1.4k
views
Sample sheet file for DiffBind
DiffBind
updated 23 months ago by
meghanapple2
• 0 • written 2.5 years ago by
Chris
▴ 20
0
votes
1
reply
907
views
How to do PFS after Voom + Limma DGE ?
RNASeqData
limma
voom
PFS
DGE
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
manuelsokolov
• 0
0
votes
1
reply
741
views
VariantFiltering error
VariantFiltering
updated 2.5 years ago by
Robert Castelo
★ 3.4k • written 2.5 years ago by
Andrew Beggs
▴ 90
0
votes
6
replies
1.5k
views
fastMNN reproducibility across machines when using Docker
batchelor
2.5 years ago
nils.eling
▴ 10
0
votes
3
replies
1.1k
views
Normalization of different input materials
Normalization
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
altuda
▴ 10
1
vote
1
reply
962
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
khaserdene99
• 0
0
votes
2
replies
1.3k
views
Drawing a heatmap with only limited genes
heatmaps
updated 2.5 years ago by
sayite3688
• 0 • written 2.5 years ago by
dania.khalid
• 0
3
votes
11
replies
2.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
alexia.brunel
• 0
0
votes
1
reply
1.2k
views
affy package and SNP arrays
crlmm
hapmapsnp6
genomewidesnp6Crlmm
affy
updated 2.5 years ago by
Kevin Blighe
★ 4.0k • written 2.5 years ago by
Vincent J. Carey, Jr.
6.7k
3
votes
2
replies
1.2k
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
CDSPARKS
▴ 30
0
votes
2
replies
760
views
BioTIP check error with hmisc
BioTIP
written 2.5 years ago by
Jennifer Yuxi
• 0
2
votes
5
replies
1.4k
views
bambu output
txdb
bambu
updated 2.5 years ago by
andre_sim
▴ 20 • written 2.5 years ago by
camilia.savitri
• 0
2
votes
8
replies
3.3k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression
DESeq2
written 2.5 years ago by
sean.mccutcheon
▴ 10
0
votes
4
replies
5.1k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 2.5 years ago by
Marco
• 0 • written 6.1 years ago by
mathai.c
• 0
0
votes
9
replies
2.7k
views
ranking the DeSeq2 results using t-values?
DESeq2
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
Theo
▴ 10
0
votes
2
replies
1.5k
views
decideTests vs topTable results
decideTests
topTable
limma
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Anna
▴ 20
0
votes
3
replies
1.5k
views
DESeq2 with nbinomGLM issues
DESeq2
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
andrebolerbarros
▴ 20
2
votes
5
replies
1.5k
views
assocTestSingle output with GxE
GENESIS
updated 2.5 years ago by
Stephanie M. Gogarten
▴ 890 • written 2.5 years ago by
SuperDad
• 0
0
votes
3
replies
1.0k
views
limma paired design
DifferentialExpression
limma
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Michael
• 0
0
votes
2
replies
1.9k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran
SingleCellExperiment
2.5 years ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
1.4k
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
suphamon.j
▴ 20
0
votes
2
replies
1.5k
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
Sukeerthi
• 0
0
votes
3
replies
2.3k
views
DESeq2 package unrecognized after downloading latest version of R: keep getting erros
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
saguiar
• 0
0
votes
3
replies
1.4k
views
Get Intron Seq
intron
BSgenome.Hsapiens.UCSC.hg38
BSgenome
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
Lillian
• 0
0
votes
6
replies
1.6k
views
plotHeatmap annotation error
plotHeatmap
scater
2.5 years ago
Alina
• 0
0
votes
2
replies
1.1k
views
RNA seq differential expression analysis
DEGseq
RNASeqData
limma
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Shaimaa Gamal
• 0
0
votes
2
replies
1.3k
views
Extracting DEG from topTags
NewWave
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
liujy4
• 0
1
vote
2
replies
1.3k
views
Error running run_app('LFQ')
LFQ
DEPpackage
run_app('LFQ')
ShinyApps
DEP
updated 2.4 years ago by
Ram
▴ 220 • written 2.5 years ago by
d.kozhevnikova
▴ 10
4
votes
7
replies
1.7k
views
Fishpond/Swish Interaction Test Error
fishpond
swish
2.5 years ago
Miguel
▴ 20
0
votes
1
reply
856
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData
DifferentialExpression
DESeq2
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
james.zhang20
• 0
46,699 results • Page
49 of 934
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Answer: segfault in edgeR glmQLFit
by
Gordon Smyth
53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. We will …
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
aqeel
• 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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