Showing : microarray • reset
1
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2
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WGCNA distance measures, clustering with TOM based on adjacency matrix type = "distance" versus correlation
wgcna microarray clustering
updated 9.8 years ago by ★ 3.0k • written 9.8 years ago by • 0
0
votes
5
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1.4k
views
annotation
Microarray Microarray
updated 9.8 years ago by • 0 • written 15.3 years ago by ▴ 110
1
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8
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1.5k
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The same statistical test for all multi omic features
limma microarray rnaseq deseq2
9.8 years ago chris86 ▴ 420
4
votes
8
replies
12k
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how to use idat file for analyses in bioconductor
microarray illumina idat
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 10
3
votes
1
reply
3.6k
views
Calculating a p value by permutation analysis
microarray
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 420
3
votes
6
replies
5.7k
views
Affymetrix miRNA 4.0 Normalization and Analysis
R Limma microarray miRNA
updated 4.6 years ago by ▴ 10 • written 9.8 years ago by ▴ 90
0
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4
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3.5k
views
Illumina ID Mapping library
lumi illumina beadarray microarray
9.8 years ago kritikamish99 ▴ 10
0
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2
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1.8k
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Ilumina microarray gene expression
microarray lumi
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 10
3
votes
10
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2.7k
views
Still need help identifying a good workflow for finding DEG in hugene 2.0 st
microarray hugene20 limma oligo
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
0
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0
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3.1k
views
DE analysis pipeline with Hugene 2.0 ST arrays
hugene20 microarray limma limma paired analysis oligo
9.8 years ago hakimelakhrass • 0
3
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3
replies
5.2k
views
Negative values after normalizing an agilent microarray dataset with limma
limma agilent offset background correction microarray
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 90
4
votes
10
replies
3.1k
views
Limma/oligo always crashing
limma microarray pd.hugene.2.0.st hugene20 oligo
9.8 years ago hakimelakhrass • 0
4
votes
6
replies
3.3k
views
limma: within-array duplicates correlation
limma mirna microarray
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
2
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2
replies
2.8k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma microarray a4Core topTable statistical inference
updated 9.8 years ago by ★ 29k • written 9.8 years ago by ▴ 840
0
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2
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2.4k
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Beadarray import of iScan generated Illumina gene expression data
Microarray GO ChipName beadarray Microarray GO ChipName beadarray
updated 9.8 years ago by • 0 • written 14.0 years ago by ▴ 350
0
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5
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2.1k
views
"oligo" package: probenames/probeinfo different from expr-set (read.cellfles): miRNA 4.0 (affy)
microarray probe annotation affy
9.8 years ago dietmar.pils • 0
4
votes
2
replies
1.7k
views
Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
microarray
updated 9.8 years ago by ★ 1.1k • written 9.8 years ago by ▴ 420
0
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1
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830
views
Interpretation of contrasts
limma microarray
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
3
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9
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3.1k
views
Annotation problem while quering hgug4112a.db with function select and duplicates for agilent microarray dataset
limma annotation agilent hgug4112a microarray
9.8 years ago Konstantinos Yeles ▴ 90
3
votes
3
replies
2.1k
views
How to define an outlier array from PCA?
microarray PCA outliers sample outliers limma
updated 9.8 years ago by ★ 29k • written 9.8 years ago by ▴ 60
1
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3
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2.2k
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Microarray data analysis for detecting alternative splicing
microarray splicing
updated 9.8 years ago by ▴ 20 • written 11.1 years ago by ▴ 40
7
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8
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5.8k
views
Model matrix for anova in limma
limma design matrix microarray limma
updated 9.8 years ago by ★ 13k • written 10.0 years ago by ▴ 60
2
votes
2
replies
9.3k
views
Convert Expression Set into a Matrix or Data Frame
microarray biobase affy R
updated 9.9 years ago by ▴ 760 • written 9.9 years ago by • 0
2
votes
5
replies
2.3k
views
fRMA: Applying mouse4302frmavecs on HT_MG-430_PM Arrays
frma microarray affiymetrix
9.9 years ago Matthias Z. ▴ 20
7
votes
4
replies
2.2k
views
very high adjusted P-vals using Illumina data from GEO
limma p values microarray illumina
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 20
2
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7
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2.2k
views
GEO MicroArray Download, Annotation, and Main Probe Filtering
microarray affy biomart
9.9 years ago anthonycolombo60 • 0
8
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8
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5.6k
views
Limma: fit a model with duplicateCorrelation()
limma microarray duplicatecorrelation technical replicates linear model
updated 9.9 years ago by ★ 29k • written 9.9 years ago by ▴ 150
4
votes
4
replies
1.8k
views
Comparing DE probes from same-platform microarrays
limma microarray meta-analysis
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 10
8
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15
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11k
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Design matrix for continuous independent variable in limma
limma microarray
9.9 years ago Linda Chaba ▴ 10
0
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1
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1.5k
views
NUSE lmFit fitPLM
Microarray limma affyPLM
updated 9.9 years ago by 53k • written 13.6 years ago by ▴ 10
2
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4
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2.8k
views
arrayQualityMetrics error: Error: Unknown parameters: cex.axis
affy microarray arrayqualitymetrics
updated 9.9 years ago by ★ 13k • written 9.9 years ago by ▴ 30
2
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2
replies
1.9k
views
Manually compute NUSE score
NUSE qualitycontrol microarray
updated 9.9 years ago by ▴ 760 • written 9.9 years ago by ▴ 40
2
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2
replies
1.6k
views
I'm looking for a filtering method that it does't use genewise variances
genefilter liimma microarray
updated 9.9 years ago by ★ 13k • written 9.9 years ago by ▴ 20
0
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1
reply
1.6k
views
Error in MetaQC R package.
r metaqc microarray geneexpression
10.0 years ago Agaz Hussain Wani ▴ 260
2
votes
6
replies
3.3k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma microarray multifactorial design duplicatecorrelation model.matrix
10.0 years ago Konstantinos Yeles ▴ 90
0
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3
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1.6k
views
intron/exon spanning probes present in the microarray
MA microarray
10.0 years ago serpalma.v ▴ 60
0
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1
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1.7k
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Appropriate selection of DE list in limma before and after implementation of arrayWeights in conjuction with duplicateCorrelation functions
limma microarray multifactorial design duplicatecorrelation arrayweights
10.0 years ago svlachavas ▴ 840
1
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1
reply
4.9k
views
Statistical power of limma vs mixed model approach to analyze microarray and differential proteomics/peptidomics experiments and Poisson/binomial mix…
RNASeq Microarray GO limma edgeR DESeq RNASeq Microarray GO limma edgeR DESeq
updated 10.0 years ago by 53k • written 12.4 years ago by ▴ 60
0
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1
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2.1k
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RMA and ComBat for 2 batches with samples in common
microarray normalization sva
updated 10.0 years ago by ▴ 650 • written 10.0 years ago by • 0
0
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1
reply
3.2k
views
WGCNA data format?
WGCNA coexpression microarray
updated 10.0 years ago by ★ 3.0k • written 10.0 years ago by • 0
0
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1
reply
2.2k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray affymetrix oligo RMA normalization
updated 10.0 years ago by 68k • written 10.0 years ago by ▴ 20
3
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1
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1.9k
views
what is fitProbeLevelModel()? doing
affymetrix oligo microarray
updated 10.0 years ago by 68k • written 10.0 years ago by ▴ 20
1
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3
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2.0k
views
confused about bioconductor/release_microarray:3.2 tag
docker microarray
10.0 years ago Karl Forner ▴ 70
1
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2
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1.8k
views
BioMart Attributes/Filters missing
microarray agilent biomart annotation
updated 10.0 years ago by 68k • written 10.0 years ago by • 0
3
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2
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1.3k
views
Non-DGE genes from Limma
limma rnaseq microarray
updated 10.0 years ago by 53k • written 10.0 years ago by ▴ 60
5
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1
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2.5k
views
Quantile normalization + sva for microarray experiment
sva quantile normalization microarray
updated 10.0 years ago by ★ 7.9k • written 10.0 years ago by ▴ 50
5
votes
5
replies
3.2k
views
Joint Preprocessing of RNA-Seq and Microarray datasets
preprocessing rnaseq microarray
updated 10.0 years ago by 53k • written 10.0 years ago by ▴ 30
0
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5
replies
3.3k
views
Load CDF files for Affymetrix ST 2.0 microarrays
microarray oligo cdf customcdf
updated 10.0 years ago by ★ 4.1k • written 10.0 years ago by ▴ 20
1
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1
reply
1.7k
views
arrayQualityMetrics for outlier detection
arrayQualityMetrics Microarray Outlier
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ▴ 10
0
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0
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1.4k
views
Background correction arguments in R package GCRMA for microarray pre-processing analysis
gcrma normalization background correction microarray
10.0 years ago svlachavas ▴ 840
2,319 results • Page 10 of 47
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Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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.
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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