Showing : microarray • reset
0
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3
replies
1.4k
views
Gene Interaction Computation
microarray gene interaction GRN
updated 10.0 years ago by ★ 3.4k • written 10.0 years ago by • 0
0
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4
replies
1.1k
views
New to analysing miccroarrays data
microarray
10.0 years ago kawess • 0
3
votes
2
replies
4.3k
views
Limma get all DE genes or filter by logFC
limma microarray rnaseq
updated 10.0 years ago by ★ 29k • written 10.0 years ago by ▴ 60
3
votes
9
replies
5.3k
views
Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
microarray normalization oligo
updated 10.1 years ago by • 0 • written 11.1 years ago by ▴ 30
2
votes
1
reply
1.9k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina bioconductor limma microarray normalization
updated 10.1 years ago by 53k • written 10.1 years ago by ▴ 90
0
votes
7
replies
2.8k
views
ExpressionSet expression values is negative from NCBI GSE data set
microarray differential gene expression
updated 10.1 years ago by 53k • written 10.1 years ago by ▴ 60
4
votes
4
replies
3.2k
views
Background correction in Illumina beadchip microarrays with limma neqc function
illumina human ht-12 v4 limma background correction BeadStudio microarray
updated 10.1 years ago by 53k • written 10.1 years ago by ▴ 840
0
votes
2
replies
1.9k
views
Help with annotating eset (Affy Arrays)
Biobase annotationdbi affy microarray
10.1 years ago rumroses12 • 0
1
vote
2
replies
1.7k
views
How do i perform chi square test in r?
microarray chisquare bioconductor bioinformatics
updated 10.1 years ago by ★ 29k • written 10.1 years ago by ▴ 10
7
votes
2
replies
2.8k
views
Appropriate explanation of the methodology behind arrayWeights function from limma R package
limma arrayWeights variance sampleQuality microarray
updated 10.1 years ago by ★ 7.9k • written 10.2 years ago by ▴ 840
0
votes
2
replies
1.6k
views
Using Nested Interaction Formula in limma
limma microarray
updated 10.1 years ago by ★ 29k • written 10.1 years ago by • 0
4
votes
12
replies
2.3k
views
Limma model for 4 factor (2*2*2*2) design to detect the factor specific effect and their interaction effect on gene expression
limma microarray
10.1 years ago baibing7713661 • 0
2
votes
8
replies
3.4k
views
illuminaHumanv4.db : annotation source, and mapping to transcript names
microarray annotation illumina human ht-12 v4
10.1 years ago VSM ▴ 120
4
votes
8
replies
2.3k
views
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma duplicatecorrelation arrayweights microarray
updated 10.1 years ago by 53k • written 10.1 years ago by ▴ 840
0
votes
1
reply
1.1k
views
Vector for Targest in Tquantile Normalization for different groups.
Microarray Microarray
updated 10.1 years ago by 53k • written 12.4 years ago by ▴ 60
1
vote
2
replies
2.1k
views
Possible methodologies of machine learning in R that can assimilate continuous variables along gene expression data for microarray classification
classification machinelearning microarray multivariate caret
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 840
0
votes
1
reply
895
views
error installing oneChannelGUI
microarray software error bioconductor
updated 10.1 years ago by 68k • written 10.1 years ago by • 0
1
vote
6
replies
1.7k
views
Effect size in non-standard linear model treatment experiment
limma microarray effect size
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ▴ 10
0
votes
1
reply
977
views
variance stabilization and normalization
R microarray normalization
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
0
votes
2
replies
2.3k
views
Loading RData files into ChAMP
microarray champ 450k
updated 10.2 years ago by • 0 • written 10.2 years ago by ▴ 10
0
votes
0
replies
1.0k
views
How to discretize expression set data ?
bioconductor chisquare discretization microarray R
10.2 years ago babumanish837 ▴ 10
0
votes
2
replies
2.3k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray illumina methylation microarray
updated 10.2 years ago by 21k • written 10.2 years ago by • 0
0
votes
1
reply
941
views
Problems with clustering a micro array data using R
microarray R clustering
updated 10.2 years ago by ▴ 130 • written 10.2 years ago by • 0
2
votes
1
reply
1.9k
views
Error in using library (affy)
affy R bioconductor microarray
updated 10.2 years ago by ★ 8.2k • written 10.2 years ago by • 0
0
votes
1
reply
738
views
Tqualtile Method Limma dose not normlize several treatment groups in a Two color experiment
limma microarray tquantile twocolor
updated 10.2 years ago by 53k • written 10.2 years ago by • 0
0
votes
5
replies
2.5k
views
MassiR Gender Prediction on Affy microarrays
microarray affy massiR
10.2 years ago t.demooij • 0
0
votes
1
reply
2.0k
views
.DTT file Affymetrix
microarray affymetrix microarrays analysis
updated 10.2 years ago by ★ 4.1k • written 10.2 years ago by • 0
0
votes
2
replies
2.1k
views
Annotation for a MoGene-2_0-st Chip/Arry Data
microarray affymetrix mouse gene arrays annotation pd.mogene.2.0.st
10.2 years ago Michaela.Fuchs • 0
1
vote
11
replies
4.8k
views
oligo package requires the annotation package pd.ht.mg.430.pm - where is it?
oligo microarray annotation
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
3
votes
9
replies
2.7k
views
Single channel analysis of two-color agilent array using limma
agilent limma twochannel microarray
updated 10.2 years ago by 53k • written 10.2 years ago by • 0
1
vote
1
reply
1.3k
views
Normalizing Gene Expression files from two different platforms
microarray cancer
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 10
1
vote
5
replies
2.0k
views
normalization of a miRNA microarray
normalization vsn eximir microarray miRNA
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 50
1
vote
1
reply
1.6k
views
How can get the GO and KEGG miRNA microarray Agilent?
go kegg limma microarray mirna
10.2 years ago santi.cabellos ▴ 10
3
votes
4
replies
4.4k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
10.2 years ago contato.carlosbau ▴ 10
2
votes
5
replies
2.5k
views
Problems with "read.agiMicroRna"
read.agiMicroRna agilent limma microarray mirna
updated 10.2 years ago by ▴ 30 • written 10.2 years ago by ▴ 10
0
votes
1
reply
1.2k
views
can not unzip Agilent data set
microarray affy and agilent
10.2 years ago shawinkarim • 0
3
votes
2
replies
2.0k
views
How to read single red channel data with Limma
limma microarray onechannel red custom
updated 10.2 years ago by 53k • written 10.2 years ago by • 0
11
votes
5
replies
3.0k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat idat microarray illumina
updated 10.2 years ago by ▴ 400 • written 10.2 years ago by ▴ 30
1
vote
6
replies
1.8k
views
Intronic sequences are the majority of the top differentially expressed genes
limma microarray normalization oligo differential gene expression
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
0
votes
4
replies
1.3k
views
Unavailable chip layout packages for `olgio` package
microarray oligo
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
2
votes
5
replies
4.4k
views
How to use t.test to select best features out of multiple features?
microarray biobase feature selection t.test R
updated 10.2 years ago by ▴ 840 • written 10.2 years ago by ▴ 10
1
vote
3
replies
3.7k
views
How to use expression set object to select genes using different gene selection methods
microarray biobase geoquery
updated 10.2 years ago by ▴ 840 • written 10.2 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Agilent Microaary EF1 data Reading and normalization
microarray R
updated 10.2 years ago by 53k • written 10.2 years ago by • 0
0
votes
1
reply
3.6k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray biobase expresiondataset r
10.2 years ago floodking • 0
6
votes
2
replies
4.1k
views
Is ComBat introducing a signal where there is none?
Microarray Clustering Cancer limma Microarray Clustering Cancer limma
12.0 years ago • updated 10.3 years ago Vegard Nygaard ▴ 120
2
votes
5
replies
2.2k
views
heatmap in R
r language microarray geneexpression
updated 10.3 years ago by ★ 1.1k • written 10.3 years ago by • 0
1
vote
1
reply
1.5k
views
gene expression data analysis
microarray geneexpression
updated 10.3 years ago by 68k • written 10.3 years ago by • 0
1
vote
5
replies
2.4k
views
Inconsistent Annotations in illuminaHumanv3.db
illuminahumanv3 annotation microarray
10.3 years ago Peter Humburg ▴ 30
0
votes
1
reply
3.6k
views
Prior plots from COMBAT
limma normalization microarray
updated 10.3 years ago by ▴ 870 • written 10.3 years ago by ▴ 420
0
votes
0
replies
1.3k
views
sqliteSendQuery(con, statement, bind.data) error using makePdInfoPackage for Nimblegen array
microarray R oligo micro array data annotation
10.3 years ago zenekzkk • 0
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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.
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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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