Showing : microarray • reset
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1
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780
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Contrast matrix with 2 columns
limma microarray
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
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0
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1.5k
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Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarr…
limma batch effect design matrix microarray confounding
8.6 years ago svlachavas ▴ 840
1
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3
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1.2k
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microarray analysis code
microarray
8.6 years ago nia ▴ 30
0
votes
2
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1.2k
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annotation in microarray analysis
microarray
8.6 years ago farahqureshi5 • 0
3
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1
reply
1.7k
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Filtering absent transcripts from Gene ST array
microarray oligo gene ST pacalls
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
0
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2
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1.5k
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Up and down regulation in LIMMA for microarray dataset
limma microarray differential gene expression
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
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1
reply
878
views
arrayExpress differential gene express analysis
deseq2 limma bioconductor edger microarray
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
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2
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1.0k
views
How do I set up the design when I have multiple regions and duplicate timepoints?
limma microarray affy
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
2
votes
7
replies
4.2k
views
Retriving Annotation for HTA2.0 using biomRt
microarray annotation biomart R
updated 8.6 years ago by ▴ 800 • written 8.6 years ago by • 0
2
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3
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1.9k
views
unusal expression level values after normalization in Affymetrix microarray experiment
microarray gcrma affy hgu133a normalization
updated 8.6 years ago by 53k • written 8.7 years ago by ▴ 50
9
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4
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7.4k
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Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
8.7 years ago Anna ▴ 50
0
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0
replies
969
views
mulcom Error in input files
mulcom error differential gene expression microarray
8.7 years ago arronar • 0
1
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1
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1.6k
views
Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set Enrichment paper?
GSEA PAGE microarray differential gene expression pathway analysis
updated 8.7 years ago by ★ 4.1k • written 8.7 years ago by • 0
2
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1
reply
1.9k
views
Differential Expression Analysis
differential gene expression microarray lumi illumina
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
0
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18
replies
7.8k
views
WGCNA error in network construction ?
microarray rnaseq
8.7 years ago m.azhar ▴ 10
5
votes
10
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3.6k
views
avereps(): 'ProbeName' or 'SystematicName' for agilent one-channel microarray?
limma microarray
updated 8.7 years ago by 53k • written 8.7 years ago by ▴ 10
6
votes
9
replies
3.0k
views
LIMMA paired analysis adjusting for two continuous variables - microarray data
limma limma design matrix limma paired analysis microarray
8.7 years ago danielle.newby • 0
2
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3
replies
3.1k
views
Normalization of Illumina Microarray Data
illumina microarray normalization
updated 8.7 years ago by 53k • written 8.7 years ago by • 0
1
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2
replies
2.5k
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how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 8.7 years ago by • 0 • written 10.7 years ago by ▴ 80
0
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0
replies
1.3k
views
How to pathway analysis of Arabidopsis thaliana organism
microarray pathview
8.7 years ago avinash gupta ▴ 130
0
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1
reply
911
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How to extract .CEL files from .DTTfile/archive
microarray .CEL fiels .DTT tools
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
1
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5
replies
2.8k
views
Removing batch effect from microarray data
removebatcheffect() microarray affymetrix microarrays
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 40
0
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2
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2.4k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray pearsoncorrelation coexpression spearman
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
0
votes
1
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1.0k
views
Problem Annotation Construction with pdInfoBuilder - Microarray Bioconductor
bioconductor pdfinfobuilder microarray nimblegene oligo
8.8 years ago • updated 8.7 years ago sorghills • 0
0
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0
replies
886
views
microarray data analysis
microarray
8.8 years ago munirapcu • 0
0
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4
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1.9k
views
huex10stv2cdf annotation file needed
cdf microarray affy
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 40
12
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7
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5.4k
views
illumina ht-12 v4 expression beadchip
microarray illumina human ht-12 v4
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 40
6
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4
replies
2.1k
views
Weird error with raw data using function boxplot after importing Affymetrix Human ST 2.0 CEL files with oligo
microarray affymetrix Human ST arrays oligo hugene20sttranscriptcluster.db
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 840
3
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6
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1.8k
views
Possible approach of compare/interpret RNA-Seq results with microarray gene expression describing the same phenotype
microarray rnaseq DEgenes meta-analysis limma
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 840
3
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6
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3.3k
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RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
8.8 years ago MOD • 0
0
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1
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1.6k
views
single probe represent multiple genes?
gcrma microarray expressionset
updated 8.8 years ago by ▴ 840 • written 8.8 years ago by ▴ 20
0
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0
replies
700
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Time series Microarray data
microarray
8.8 years ago greevaphilip7 • 0
6
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1
reply
12k
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How to combine multiple probes representing a single gene?
microarray affy eset
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 20
9
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6
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4.6k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray oligo affycoretools pd.hugene.2.0.st hugene20sttranscriptcluster.db
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 840
0
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3
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4.6k
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How do I choose between using affy or oligo package for preprocessing microarrays?
microarray affymetrix microarrays affy oligo
updated 4.7 years ago by 68k • written 8.8 years ago by • 0
0
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1
reply
1.5k
views
annotation of agillent array G3 Human Gene Expression v3 8x50
microarray annotation agilent
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 40
1
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2
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1.4k
views
Correlating DNA methylation and Illumina gene expression microarray data
microarray HM450 dna methylation cohcap
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 10
10
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5
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3.4k
views
One replicate (one-color OR two-color) is enough to use Limma?
limma microarray
8.9 years ago kevin.m.hao ▴ 10
2
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2
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1.9k
views
SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
8.9 years ago Brian Smith ▴ 120
0
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3
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1.3k
views
Custom cdf and Ensemble
customcdf R microarray
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
0
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1
reply
1.3k
views
Custom cdf files and genes
cdf microarray r3.2.2
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
3
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2
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1.6k
views
Difficulty for analysis of GSE7864
limma microarray bioconductor ncbi geo
updated 8.9 years ago by 53k • written 8.9 years ago by ▴ 10
2
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1
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4.0k
views
Heatmap error: 'ColSideColors' must be a character vector of length ncol(x)
microarray limma Bioconductor
updated 8.9 years ago by 53k • written 8.9 years ago by • 0
0
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3
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1.2k
views
R script for getting Common DEG genes from all comparisons by limma analysis
limma bioconductor Microarray R
updated 8.9 years ago by 53k • written 8.9 years ago by • 0
8
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11
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2.8k
views
Creating design matrix in LIMMA
limma microarray R
8.9 years ago sgblackpearl • 0
5
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11
replies
6.3k
views
Duplicate gene ID's returned from limma microarray analysis
limma microarray
updated 3.6 years ago by 53k • written 8.9 years ago by ▴ 80
0
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1
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654
views
TopGO code Line
microarray
8.9 years ago lolaferu • 0
1
vote
3
replies
2.0k
views
WGCNA Co-expression
microarray differential gene expression module
updated 8.9 years ago by ★ 3.0k • written 8.9 years ago by • 0
0
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0
replies
1.2k
views
Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
8.9 years ago shaheryar • 0
2
votes
4
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1.5k
views
What are all the different methods available for identifying the DEG?
limma microarray
updated 8.9 years ago by 53k • written 8.9 years ago by ▴ 20
2,319 results • Page 7 of 47
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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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