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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
2.6 years ago
sreeshmaraj72
• 0
4
votes
8
replies
2.1k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
2.6 years ago • updated 2.5 years ago
Habil Zare
▴ 200
5
votes
8
replies
3.1k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 2.0 years ago by
Shaimaa Gamal
• 0 • written 2.6 years ago by
pg45863
▴ 10
1
vote
0
replies
979
views
News:
Last Week to Nominate for Bioc2023 Awards!
Bioconductor
Bioc2023
Recognition
Awards
2.6 years ago
shepherl
4.2k
0
votes
0
replies
896
views
News:
Junior Developer or New Package Developer Award
Bioconductor
Recognition
Bioc2023
Awards
2.6 years ago
shepherl
4.2k
0
votes
0
replies
1.0k
views
News:
Bioconductor Community Engagement, Outreach, and Diversity Award
Awards
Bioconductor
Bioc2023
Recognition
2.7 years ago • updated 2.6 years ago
shepherl
4.2k
0
votes
0
replies
995
views
News:
Bioconductor Long-term Contribution Award
Bioc2023
Bioconductor
Awards
Recognition
2.6 years ago
shepherl
4.2k
0
votes
0
replies
881
views
News:
Nominations for Bioconductor 2023 Awards!
Awards
Bioconductor
Bioc2023
Recognition
2.7 years ago • updated 2.6 years ago
shepherl
4.2k
0
votes
1
reply
985
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 2.6 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
simon
• 0
1
vote
1
reply
1.6k
views
Could not find function ".read_block_OLD"
DelayedArray
S4Arrays
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
xiuwen.zheng
• 0
0
votes
0
replies
1.0k
views
News:
course - single-cell RNAseq data analysis with R and Bioconductor
Workshop
scRNAseq
2.6 years ago
info
▴ 10
2
votes
3
replies
3.9k
views
Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
Hyoann
▴ 20
3
votes
7
replies
2.8k
views
Installing densvis on a Singularity container
densvis
docker
updated 2.6 years ago by
alan.ocallaghan
▴ 160 • written 2.6 years ago by
James W. MacDonald
68k
2
votes
4
replies
3.0k
views
SummarizedExperiment is now warning on attach about `read_block` namespace conflict
SummarizedExperiment
S4Arrays
DelayedArray
updated 2.5 years ago by
Hervé Pagès
16k • written 2.6 years ago by
Michael Steinbaugh
▴ 90
0
votes
1
reply
745
views
msqrob2 outputs (Protein IDs?)
msqrob2
updated 2.6 years ago by
Laurent Gatto
1.6k • written 2.6 years ago by
richard.naylor-2
• 0
2
votes
9
replies
7.1k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 7.8 years ago by
klalit1803
▴ 10
0
votes
1
reply
887
views
CI for logCPM (fitted values)
RNAseq
edgeR
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Lina
▴ 10
0
votes
0
replies
564
views
'ZygosityPredictor's dependency 'datastructures' missing in R 4.3.0
ZygosityPredictor
updated 2.6 years ago by
Kevin Blighe
★ 4.0k • written 2.6 years ago by
Marc
• 0
0
votes
2
replies
1.0k
views
No compilation on Windows y compilation on linux
Devel
PackageType
deve
2.6 years ago • updated 2.5 years ago
Franck RICHARD
• 0
3
votes
3
replies
1.9k
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression
DESeq2
updated 2.6 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
tinattn.nguyen
▴ 20
1
vote
2
replies
1.8k
views
Batch effect between biological replicates
BatchEffect
DESeq2
2.6 years ago
gtechbio
▴ 10
1
vote
3
replies
1.1k
views
Find if one gene has a significantly different Log2FC than a different gene
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Matt
• 0
0
votes
3
replies
1.4k
views
Dispersion outliers genes
Dispersion
DESeq2
2.6 years ago
raya.fai
▴ 60
0
votes
0
replies
1.2k
views
Job:
PostDoc in Computational Biology at Leibniz Institute for Environmental Medicine
Aging
Epigenome
Bioinformatics
Mergeomics
Evolution
2.6 years ago
arne.sahm
• 0
0
votes
0
replies
800
views
Help with Diffbind result
DiffBind
2.6 years ago
Chris
▴ 20
0
votes
1
reply
1.2k
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Yijing
• 0
0
votes
2
replies
2.0k
views
about baseMean in DEseq2
DESeq2
written 4.4 years ago by
Bogdan
▴ 670
3
votes
3
replies
1.5k
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 3.0 years ago by
Bioinformatics-414
• 0
3
votes
7
replies
2.5k
views
"Degree values are the same for all nodes in a network imported from WGCNA to Cytoscape using RCy3. Seeking insights and potential causes."
Cytoscape
RCy3
Networkvisualization
WGCNA
2.6 years ago
Ortega-C
▴ 10
0
votes
3
replies
1.2k
views
Error in champ.load() function
ChAMP
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Monalisa
• 0
0
votes
3
replies
1.8k
views
Batch correction using control probes in EPIC array data
RnBeads
minfiData
minfi
EPICarray
updated 2.6 years ago by
Basti
▴ 780 • written 2.6 years ago by
Jitendra
▴ 10
0
votes
0
replies
1.5k
views
News:
Join the Technical Advisory Board
Bioconductor
News
Organization
2.6 years ago
Maria Doyle
▴ 110
0
votes
2
replies
1.1k
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 21 months ago by
CHEN
• 0 • written 2.6 years ago by
Saanchi
• 0
0
votes
2
replies
1.2k
views
Accounting for technical replicates in DESeq2
DESeq2
updated 2.6 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
sara.p
• 0
0
votes
1
reply
1.2k
views
LIMMA: design with paired samples within and across treatments
DifferentialExpression
limma
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
mbyvcm
• 0
0
votes
0
replies
755
views
IsoformSwitchAnalyzer
Isoform
IsoformSwitchAnalyzeR
2.6 years ago
Craig
• 0
0
votes
2
replies
792
views
justRMA or similar for normalization with hg133a and hg133plus
hgu133plus2CellScore
hthgu133a.db
affydata
2.6 years ago
Susanna
• 0
0
votes
4
replies
2.2k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano
RNASeqData
DifferentialExpression
2.6 years ago
ruba-mahmoud
• 0
0
votes
2
replies
1.7k
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest
ChAMP
annotation
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Matilda
• 0
0
votes
2
replies
1.2k
views
Docker usage with Trio Bioconductor Package
VariantAnnotation
docker
trio
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
sethberke
• 0
1
vote
1
reply
853
views
How to determine if any samples are outliers in PCA? What is the criteria?
"PCA"
miaSim
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
Yijing
• 0
3
votes
4
replies
1.1k
views
Anova table edgeR limma
limma
RNASeq
edgeR
2.6 years ago
KATHERINE CHUERE NUNES
• 0
0
votes
0
replies
595
views
How to get the class ID of patients using ConsensusClusterPlus
ConsensusClusterPlus
2.6 years ago
hsin hsiung
• 0
3
votes
1
reply
1.0k
views
Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Thomas
• 0
0
votes
0
replies
702
views
High Memory Usage when running FRASER's countRNAData
FRASER
2.6 years ago
jbendik
• 0
0
votes
4
replies
2.1k
views
BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)
Annotation
2.6 years ago
Michael Steinbaugh
▴ 90
1
vote
1
reply
971
views
`MOFAobject@expectations` is empty list
MOFA2
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Dan
• 0
0
votes
3
replies
1.3k
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq
normalization
PCR_efficiency
bias
intrasample_comparison
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
FedeXandeR
• 0
0
votes
1
reply
930
views
Calculate RPKMs and Output proteins pass the cutoff into FASTA file ... Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : i…
customProDB
easyrun
error
mm10
Mus_musculus_Data
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Esraa
• 0
0
votes
3
replies
1.5k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
FedeXandeR
• 0
46,698 results • Page
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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…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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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