Showing : microarray • reset
4
votes
7
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2.2k
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Microarray data preprocessing and differentially expressed genes
microarray affy limma
updated 9.5 years ago by ▴ 610 • written 9.5 years ago by • 0
1
vote
1
reply
1.3k
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Format of data matrix, probedata and phenodata for building Rnits object ?
Rnits microarray limma
9.5 years ago eu_sanisa • 0
4
votes
1
reply
859
views
How to fit a regression for a time series array experiment with limma?
limma microarray
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 420
1
vote
2
replies
907
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Best approach to analyse this time series experiment
microarray
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 420
4
votes
4
replies
2.3k
views
Limma Elist subsetting
microarray limma subsetting
9.5 years ago arfranco ▴ 130
0
votes
0
replies
966
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Remote bioinformatics assistance for severely visually impaired bioinformatics graduate student needed
limma microarray rna-seq
9.5 years ago Thomas.F.Hahn2 • 0
0
votes
0
replies
1.4k
views
Job: Remote bioinformatics assistance for severely visually impaired bioinformatics graduate student needed
microarray limma affymetrix microarrays r microarray affy rna-seq Job
9.5 years ago Thomas.F.Hahn2 • 0
2
votes
2
replies
1.5k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 19 months ago by • 0 • written 9.5 years ago by • 0
2
votes
2
replies
1.9k
views
Batch effect removal
microarray limma removebatcheffect()
9.5 years ago Eleni Christodoulou ▴ 150
0
votes
0
replies
1.3k
views
Help in interpreting the plot of the function plotRLDF in limma package for microarray dataset concerning two categorical classes
limma plotRLDF microarray classification linear discriminant function
9.5 years ago svlachavas ▴ 840
1
vote
2
replies
933
views
how/what to use to perform Differential Expression Gene if log2 available?
microarray limma edgeR
updated 9.5 years ago by 53k • written 9.5 years ago by • 0
0
votes
1
reply
1.4k
views
Questions about the correct implementation of the function plotRLDF from R package limma regarding classification of a microarray dataset
limma microarray plotRLDF classification
9.5 years ago svlachavas ▴ 840
5
votes
2
replies
13k
views
lowess vs. loess
Microarray Normalization
updated 9.5 years ago by 53k • written 22.3 years ago by ▴ 30
1
vote
3
replies
2.0k
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma microarray linear model statistical modeling model.matrix
9.5 years ago christopher.clarskon15 ▴ 20
6
votes
11
replies
2.8k
views
microarray data analsis with limma?
limma genepix microarray agilent microarrays
9.5 years ago Mehmet Ilyas Cosacak • 0
1
vote
3
replies
2.5k
views
WGCNA clustering configuration
clustering wgcna microarray
updated 9.5 years ago by ★ 3.0k • written 9.5 years ago by ▴ 760
2
votes
6
replies
2.7k
views
Using TCGAbiolinks for exon and oligonucleotide level microarray
tcga tcgabiolinks microarray exons oligonucleotide
updated 9.5 years ago by ▴ 270 • written 9.6 years ago by • 0
5
votes
10
replies
5.5k
views
Interpretation of results for treat & topTreat functions from limma regarding microarray abalysis
limma treat topTreat microarray
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 840
2
votes
1
reply
3.0k
views
Using Limma to identify any differences between multiple treatment groups (without making pairwise comparisons)
microarray limma multiple treatments lfc
updated 9.5 years ago by ★ 29k • written 9.5 years ago by • 0
0
votes
0
replies
1.3k
views
Lumi Control Data
lumi illumina microarray
9.6 years ago m.a.bentley • 0
0
votes
1
reply
1.9k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 9.6 years ago by 68k • written 9.6 years ago by • 0
0
votes
0
replies
987
views
normalizing gene expression data with TCGAbiolinks
microarray tcgabiolinks rnaseq
9.6 years ago Fernando • 0
1
vote
3
replies
1.6k
views
How to compute Gene Regulatory Network on microarraay data
microarray GRN gene interaction
updated 9.6 years ago by ▴ 420 • written 9.6 years ago by • 0
0
votes
1
reply
1.2k
views
How to compute Microarray gene interaction
microarray gene interaction GRN r
updated 9.6 years ago by ▴ 420 • written 9.6 years ago by • 0
1
vote
2
replies
1.4k
views
package ‘org.At.tair.db’ could not be loaded
microarray
updated 9.6 years ago by 25k • written 9.6 years ago by • 0
8
votes
3
replies
4.0k
views
Differing topTable() results with Limma with and without specifying coefficient
limma microarray statistics
updated 9.6 years ago by 53k • written 9.6 years ago by • 0
1
vote
2
replies
3.0k
views
TCGAbiolinks data download problem
cancer microarray bioconductor tcgabiolinks
9.6 years ago Fernando • 0
0
votes
1
reply
1.7k
views
'could not find function "R (>= 2.1"' while trying https://bioconductor.org/packages/3.2/bioc, trying https://bioconductor.org/packages/3.1/bioc …
cancer probe microarray
updated 9.6 years ago by 25k • written 9.6 years ago by • 0
7
votes
2
replies
2.0k
views
limma experimental design
limma microarray
updated 9.6 years ago by 53k • written 9.6 years ago by ▴ 20
5
votes
8
replies
1.8k
views
designing matrices practice
limma microarray
9.7 years ago • updated 9.6 years ago christopher.clarskon15 ▴ 20
2
votes
3
replies
1.5k
views
Adapting old Workshop to recent changes of the Limma package
limma microarray tutorial
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 40
0
votes
0
replies
1.3k
views
Correct creation of design matrix in limma for testing a specific comparison of interest in a microarray dataset
limma microarray design and contrast matrix
9.7 years ago svlachavas ▴ 840
8
votes
5
replies
3.7k
views
Limma un moderated t-test
limma microarray
updated 9.7 years ago by ★ 1.1k • written 9.7 years ago by ▴ 420
0
votes
1
reply
1.3k
views
Processing iScan raw data without perBeadFile.txt
microarray beadarray
updated 9.7 years ago by ★ 6.6k • written 9.7 years ago by • 0
1
vote
2
replies
2.6k
views
Further analysis of methylation microarrays data (Illumina - idat) after reading by illuminaio package
limma lumi illuminaio illimina 450k methylation microarray
9.7 years ago Adam • 0
0
votes
0
replies
1.2k
views
Regarding the package RankProd
microarray rankprod
9.7 years ago sancharisircar24 • 0
1
vote
7
replies
3.0k
views
CellCODE not installing
differential gene expression microarray
9.7 years ago christopher.clarskon15 ▴ 20
3
votes
6
replies
3.0k
views
Comparison of DE lists from different datasets of same microarray platform
microarray DE-comparison meta-analysis scatter-plot limma
9.7 years ago Konstantinos Yeles ▴ 90
3
votes
3
replies
3.3k
views
Problem using RMA Method in 'Oligo' with HTAFeatureset Objects
affymetrix microarrays microarray pd.hta.2.0 oligo rma
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
8
votes
10
replies
6.0k
views
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
limma topTable confidence interval effect size microarray
updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 90
2
votes
6
replies
3.2k
views
Density plots microarray
microarray limma normalization densityplot
updated 9.7 years ago by ★ 1.1k • written 9.7 years ago by ▴ 150
2
votes
3
replies
3.4k
views
Adjusted p-value output from Limma different from output using p.adjust?
Limma R microarray
9.7 years ago Cale Reid ▴ 10
8
votes
12
replies
4.9k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma microarray interaction model multiple factor design makeContrasts
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 840
0
votes
1
reply
1.2k
views
Really weird results when I filter this new data that I have, script has worked on two previous data sets.
microarray limma genefilter
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
0
votes
0
replies
968
views
Mouse ST 2.1 noncoding
microarray affymetrix microarrays
9.8 years ago miquel.garcia • 0
0
votes
1
reply
1.3k
views
PGSEA Steps Using Bioconductor
microarray pgsea
updated 9.8 years ago by ★ 8.2k • written 9.8 years ago by • 0
0
votes
3
replies
2.8k
views
neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 110
0
votes
2
replies
1.7k
views
clustering analysis of illumina microarray gene expression data
clustering illumina microarray
9.8 years ago kritikamish99 ▴ 10
2
votes
7
replies
5.7k
views
How to create "trait data" file for WGCNA
wgcna coexpression correlation microarray
updated 9.8 years ago by ★ 3.0k • written 9.8 years ago by ▴ 20
1
vote
2
replies
5.5k
views
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
2,319 results • Page 9 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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