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Showing :
microarray
•
reset
2
votes
2
replies
741
views
HOW TO USE LIMMA PACKAGE
limma
microarray
updated 6.7 years ago by
Aaron Lun
★ 29k • written 6.7 years ago by
singhjay
▴ 10
0
votes
1
reply
1.1k
views
differential expression analysis of rice
microarray
differential expression analysis
GPL2025
affymetrix
updated 6.7 years ago by
Aaron Lun
★ 29k • written 6.7 years ago by
pratikshasharma47
• 0
0
votes
1
reply
980
views
Differentially expressed genes in rice affymetrix data and annotation
affy
microarray
differentially expresed genes
limma
annotation
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
pratikshasharma47
• 0
2
votes
27
replies
3.6k
views
Applying NetAffx biological annotation to Affymetrix gene expression dataset
microarray
annotation
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
lm795
▴ 10
0
votes
0
replies
853
views
fData slot in gene expression analysis
affy
microarray
gene expression analysis
6.7 years ago
pratikshasharma47
• 0
1
vote
1
reply
597
views
differential expression analysis of merged dataset
microarray
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
pratikshasharma47
• 0
2
votes
2
replies
1.9k
views
AnnotationData Packages for GPL2507 Sentrix Human-6 Expression BeadChip
microarray
annotation
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
kankejia0703
• 0
0
votes
2
replies
919
views
error after normalizing data
microarray
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
vasukiperumalla
• 0
0
votes
0
replies
1.6k
views
Beta values and M values cluster differently
methylationEPIC
minfi
microarray
epigenetics
EPIC
6.7 years ago
firestar
▴ 20
0
votes
0
replies
1.1k
views
Best normalisation method
microarray
methylationEPIC
epigenetics
minfi
EPIC
6.7 years ago
firestar
▴ 20
4
votes
4
replies
1.9k
views
Illumina Methylation 27k minfi
microarray
methylation
illumina27k
minfi
updated 6.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 6.7 years ago by
laurenz.holcik
• 0
0
votes
0
replies
1.3k
views
I am trying to recreate results from an Alzheimer's paper but I can't figure out my linear regression model
limma
microarray
differential gene expression
linear regression
edger
6.7 years ago
ravelarvargas
• 0
0
votes
3
replies
1.4k
views
~50% significant genes from RNA (NanoString) Differential Expression Analysis
limma
microarray
voom
6.7 years ago
rueben.bautista7
• 0
0
votes
1
reply
2.0k
views
How to convert a SingleCellExperiment into an ExpressionSet object?
microarray
annotation
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
FB
• 0
1
vote
6
replies
1.9k
views
Error while running affylmGUI
microarray
limma
affy
affylmGUI
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
devyani66
• 0
1
vote
4
replies
1.8k
views
I am having trouble recreating the linear regression results published in an Alzheimer's paper
limma
edger
linear regression
microarray
differential gene expression
6.7 years ago
ravelarvargas
• 0
0
votes
1
reply
842
views
Meta_analysis of microarray data
microarray
microarray data
Meta Analysis
platform
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
Jamal
• 0
2
votes
1
reply
923
views
When to Correct for Cell Type Heterogeneity in ChAMP Pipeline
microarray
updated 4.9 years ago by
Ankit
▴ 20 • written 6.8 years ago by
Gurkenkönig
▴ 10
0
votes
0
replies
797
views
ChAMP champ.norm BMIQ produces differing results
microarray
normalization
6.8 years ago
Gurkenkönig
▴ 10
0
votes
0
replies
977
views
How to merging multiple GSEs with different GPLs?
microarray
probe
R
6.8 years ago
maryam.sabet
• 0
11
votes
4
replies
2.7k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 2.2 years ago by
Gordon Smyth
53k • written 6.8 years ago by
tleona3
• 0
1
vote
1
reply
830
views
"0" p value from Rosetta resolver?
microarray
affy
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
vibhusahni
• 0
1
vote
2
replies
1.3k
views
Meta-analysis of RNAseq data
RNAseq
meta-analysis
microarray
public data sets
updated 6.8 years ago by
alexvpickering
▴ 110 • written 6.8 years ago by
Vladimir Krasikov
▴ 90
3
votes
6
replies
3.9k
views
Limma design/contrast correct?
limma
microarray
design
paired
mixed model
updated 6.8 years ago by
Aaron Lun
★ 29k • written 6.8 years ago by
rasmus.agren
• 0
0
votes
1
reply
1.5k
views
MCLUST: finding the best number of Gaussian components to fit my data
software error
microarray
probe
annotation
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
travascio.andrea91
• 0
0
votes
1
reply
1.2k
views
Array quality metrics for large sample size
microarray
quality
updated 6.8 years ago by
Wolfgang Huber
★ 13k • written 6.8 years ago by
RV
▴ 10
1
vote
2
replies
797
views
How to find the expression values of genes matched by multiple probes in 2-channel microarray?
microarray
annotation
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
KCLiv
▴ 20
1
vote
8
replies
2.2k
views
how can I calculate FDR with no replicate
microarray
edger
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
Bioinformatics
▴ 30
2
votes
4
replies
1.4k
views
Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(colors)):
Wolfgang Huber
microarray
6.8 years ago
RV
▴ 10
1
vote
4
replies
1.2k
views
How many probe sequences per spot
microarray
6.8 years ago
w.abram
• 0
2
votes
2
replies
1.2k
views
Limma import array layout GenePix files
limma
microarray
layout
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
Guillaume Robert
• 0
0
votes
0
replies
669
views
Error in Champ for Bioconductor and ChAMP.Block() analysis 450K methylation data
normalization
microarray
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
15936296950
• 0
7
votes
13
replies
2.7k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma
microarray
hugeneST
batch effect
DE
updated 6.8 years ago by
Ryan C. Thompson
★ 7.9k • written 6.8 years ago by
svlachavas
▴ 840
2
votes
2
replies
1.1k
views
Limma filtering low expressed probes
limma
microarray
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
Guillaume Robert
• 0
7
votes
6
replies
2.5k
views
Limma import .gpr file error
limma
gpr
microarray
updated 6.9 years ago by
Gordon Smyth
53k • written 6.9 years ago by
Guillaume Robert
• 0
2
votes
2
replies
1.4k
views
aafTableAnn complaining about NAs when there are none
aafTableAnn
microarray
annafy
hgu133plus2.db
updated 6.9 years ago by
James W. MacDonald
68k • written 6.9 years ago by
maxininfa
• 0
0
votes
1
reply
1.3k
views
Creating GRanges object
microarray
minfi
GenomicRatio
GRanges
Methylation
updated 6.9 years ago by
James W. MacDonald
68k • written 6.9 years ago by
lalchungnungabt17
• 0
3
votes
7
replies
1.7k
views
Limma analysis, controlling for Donors.
limma
r
microarray
updated 6.9 years ago by
Gordon Smyth
53k • written 6.9 years ago by
reubenmcgregor88
• 0
0
votes
3
replies
2.3k
views
Algorithm for between and within microarray normalisation (for meta-analysis).
microarray
meta-analysis
gene expression
updated 6.9 years ago by
Bioconductor Community
0 • written 9.3 years ago by
StephK
▴ 70
0
votes
1
reply
1.6k
views
Meta_analysis of different platforms of microarray data
microarray
meta analysis
cancer
Software
R
updated 6.9 years ago by
James W. MacDonald
68k • written 6.9 years ago by
Jamal
• 0
1
vote
3
replies
3.3k
views
WGCNA: cleaning for sample outliers
microarray
gene network
WGCNA
updated 6.9 years ago by
Bioconductor Community
0 • written 6.9 years ago by
GENOMIC_region
• 0
2
votes
2
replies
2.5k
views
Array Normalization on focussed array in Limma using R
limma
microarray
r
updated 6.9 years ago by
Gordon Smyth
53k • written 6.9 years ago by
reubenmcgregor88
• 0
1
vote
12
replies
3.3k
views
avereps with probes mapping to multiple genes (Agilent dual color microarray)
limma
avereps
probe mapping
microarray
Agilent
updated 6.9 years ago by
Gordon Smyth
53k • written 6.9 years ago by
wd
▴ 30
1
vote
2
replies
1.9k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 7.0 years ago by
Ou, Jianhong
★ 1.3k • written 7.0 years ago by
Adam_M
• 0
4
votes
4
replies
1.6k
views
arrayQualityMetrics in reading HTAfeatureSet read by oligo package
microarray
hta2.0
arrayqualitymetrics
updated 7.0 years ago by
Mike Smith
★ 6.6k • written 7.0 years ago by
RV
▴ 10
1
vote
3
replies
1.5k
views
Two microarrays merging (different experiments) - Error with esets (inSilicoMerging package)
inSilicoMerging
microarray
affymetrix microarrays
updated 7.0 years ago by
James W. MacDonald
68k • written 7.0 years ago by
Adam_M
• 0
0
votes
6
replies
1.3k
views
minfi R package for methylation analysis of infinium 450K microarray data
microarray
bioconductor
updated 7.0 years ago by
James W. MacDonald
68k • written 7.0 years ago by
sinha.puja
▴ 10
0
votes
1
reply
3.8k
views
Timeout was reached error in GEOquery package
R
microarray
software error
updated 7.0 years ago by
Kevin Blighe
★ 4.0k • written 7.0 years ago by
morteza.hadizade
▴ 10
0
votes
0
replies
909
views
Filtering probesets for HuEx ST1.0 after probeset normalization
microarray
exons
probefiltering
7.1 years ago
GENOMIC_region
• 0
1
vote
0
replies
2.5k
views
Exploring upstream regulators (transcription factors, drugs, etc) of transcripts in R
microarray
bioconductor
cytoscape
mapfromtranscripts
7.1 years ago
lm795
▴ 10
2,319 results • Page
4 of 47
Recent ...
Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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