Showing : lumi • reset
3
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9
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7.3k
views
Illumina Expression analysis from iDAT files
beadarray lumi illuminaio idat
updated 4.0 years ago by 53k • written 12.0 years ago by 21k
0
votes
10
replies
3.0k
views
MethyLumiM to MethyLumiSet?
convert lumi methylumi minfi wateRmelon convert lumi methylumi minfi wateRmelon
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ▴ 190
0
votes
2
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4.8k
views
Annotate - gene name to ENSEMBL
Microarray GO lumi Microarray GO lumi
updated 12.1 years ago by ▴ 400 • written 12.1 years ago by ▴ 180
0
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0
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1.2k
views
MethyLumiM to MethyLumiSet?
convert lumi methylumi convert lumi methylumi
12.1 years ago Allegra Petti ▴ 120
0
votes
3
replies
2.0k
views
mifi unable to install by bioLite
lumi lumi
updated 12.1 years ago by ★ 4.2k • written 12.2 years ago by ▴ 30
0
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0
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1.1k
views
variation between chips - neqc()
Microarray Normalization probe limma lumi Microarray Normalization probe limma lumi
12.2 years ago Rao,Xiayu ▴ 550
0
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1
reply
2.5k
views
Control probe QC plots for Infinium 450k chips (lumi, minfi...)
Annotation probe lumi minfi Annotation probe lumi minfi
updated 12.3 years ago by ★ 4.2k • written 12.3 years ago by ▴ 90
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0
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1.2k
views
GenomeStudio output and lumi
lumi lumi
12.3 years ago Sanja Rogic ▴ 10
0
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2
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2.2k
views
Reading Illumina data from GenomeStudio in limma
probe lumi probe lumi
updated 12.3 years ago by ★ 3.6k • written 12.3 years ago by ★ 13k
0
votes
1
reply
1.9k
views
problem with 'FDb.InfiniumMethylation.hg19'
BSgenome BSgenome lumi methylumi BSgenome BSgenome lumi methylumi
updated 12.4 years ago by ▴ 120 • written 12.4 years ago by 68k
0
votes
2
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1.7k
views
lumiR returns ExpressionSet object instead of LumiBatch
GO Mus musculus BSgenome BSgenome lumi GO Mus musculus BSgenome BSgenome lumi
updated 12.4 years ago by ▴ 440 • written 12.4 years ago by ★ 13k
0
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4
replies
1.2k
views
proper way to handle small changes from different package versions
lumi lumi
updated 12.5 years ago by 68k • written 12.5 years ago by ▴ 360
0
votes
0
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1.6k
views
How do I background correct an Illumina eset without using lumiB
Microarray probe limma PROcess convert beadarray lumi Microarray probe limma PROcess
12.5 years ago Gordon Smyth 53k
0
votes
1
reply
1.7k
views
How do I background correct an Illumina eset without using lumiB?
Microarray probe PROcess convert beadarray lumi Microarray probe PROcess convert lumi
updated 12.5 years ago by ▴ 440 • written 12.5 years ago by ★ 13k
0
votes
0
replies
2.3k
views
how to use MethyLumiM object in BMIQ(wateRmelon)
lumi methylumi lumi methylumi
12.6 years ago Guest User ★ 13k
0
votes
1
reply
1.1k
views
Pre-processing and probe removal in lumi
lumi lumi
updated 12.8 years ago by ▴ 480 • written 12.8 years ago by ▴ 30
0
votes
1
reply
4.6k
views
Problem installing packages on new R
limma beadarray lumi arrayMvout limma beadarray lumi arrayMvout
updated 12.8 years ago by 68k • written 12.8 years ago by ▴ 10
0
votes
0
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1.5k
views
importing data problem with methyAnalysis package
Biophysics Annotation Preprocessing annotate lumi methyAnalysis Biophysics Annotation lumi
12.9 years ago Pan Du ▴ 440
0
votes
0
replies
762
views
lumi NuID to UCSC, for example "xl5dFtdFTQCRSSkbwc" to something like "uc002qsd.4"
lumi lumi
13.0 years ago Fenton Christopher Graham ▴ 90
0
votes
2
replies
2.1k
views
arrayQualityMetrics and lumi - failure to load in R2.15.1 windows
lumi arrayQualityMetrics lumi arrayQualityMetrics
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 480
0
votes
5
replies
1.8k
views
gdata affects LumiBatch::combine method
lumi lumi
updated 13.2 years ago by 25k • written 13.2 years ago by ▴ 910
0
votes
2
replies
1.7k
views
Generating GEO submission files from beadarray summary data
beadarray lumi PROMISE beadarray lumi PROMISE
updated 13.2 years ago by ★ 1.1k • written 13.2 years ago by ★ 4.2k
0
votes
2
replies
1.6k
views
Error, while using produceGEOSampleInfoTemplate
beadarray lumi PROMISE beadarray lumi PROMISE
updated 13.2 years ago by ★ 4.2k • written 13.2 years ago by ▴ 350
0
votes
3
replies
2.4k
views
problems installing lumi
lumi lumi
updated 13.2 years ago by ▴ 440 • written 13.2 years ago by ▴ 110
0
votes
1
reply
1.1k
views
lumi - Heatmap
lumi lumi
updated 13.3 years ago by 21k • written 13.3 years ago by ▴ 350
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4
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1.6k
views
#Identify differentially expressed genes
limma lumi limma lumi
updated 13.3 years ago by 53k • written 13.3 years ago by ▴ 350
0
votes
4
replies
3.5k
views
Error : package slot missing from signature for generic
Biobase lumi oligoClasses Biobase lumi oligoClasses
13.3 years ago Mark Cowley ▴ 910
0
votes
0
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1.1k
views
lumi - limma - geneSymbol and geneName N/A
limma lumi limma lumi
13.3 years ago Paolo Kunderfranco ▴ 350
0
votes
1
reply
1.0k
views
lumi - limma - geneSymbol/geneName
limma lumi limma lumi
updated 13.4 years ago by ★ 7.2k • written 13.3 years ago by ▴ 350
0
votes
1
reply
1.6k
views
lumi - construct a design matrix
lumi CMA lumi CMA
updated 13.4 years ago by ▴ 260 • written 13.4 years ago by ▴ 350
0
votes
3
replies
1.8k
views
Simple conceptual question
Normalization lumi Normalization lumi
updated 13.4 years ago by ▴ 380 • written 13.4 years ago by ▴ 440
0
votes
0
replies
745
views
Question about lumiMethyN() in lumi package
probe lumi probe lumi
13.5 years ago Pan Du ▴ 440
0
votes
0
replies
1.1k
views
output from "getChipInfo" prevents Illumina ProbeID conversion
Annotation Normalization convert lumi Annotation Normalization convert lumi
13.5 years ago Pan Du ▴ 440
0
votes
0
replies
1.6k
views
Illumina beadarray analysis with lumi
Normalization Preprocessing probe PROcess beadarray lumi Normalization Preprocessing probe
13.6 years ago Ahmet ZEHIR ▴ 50
0
votes
0
replies
1.0k
views
Question about Infinium Methylation normalization using lumi package
Normalization probe lumi Normalization probe lumi
13.6 years ago Pan Du ▴ 440
0
votes
1
reply
1.1k
views
Question about using lumi package
Cancer lumi Cancer lumi
updated 13.7 years ago by ▴ 440 • written 13.7 years ago by ▴ 10
0
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0
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1.3k
views
Bioconductor Digest, Vol 110, Issue 11
Normalization Cancer lumi methylumi Normalization Cancer lumi methylumi
13.7 years ago Pan Du ▴ 440
0
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0
replies
1.3k
views
Help with lumi R package
Microarray lumi Microarray lumi
13.7 years ago Minyue Wang ▴ 10
0
votes
3
replies
1.4k
views
some questions about lumi package and Illumina arrays
Normalization probe limma lumi Normalization probe limma lumi
updated 13.7 years ago by ★ 3.6k • written 13.7 years ago by ▴ 840
0
votes
0
replies
888
views
Get negative control probes in lumiBarnes data set
beadarray lumi beadarray lumi
13.7 years ago Guest User ★ 13k
0
votes
1
reply
1.2k
views
LumiT VST error
lumi lumi
updated 13.7 years ago by ▴ 440 • written 13.7 years ago by ▴ 350
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0
replies
762
views
Bioconductor Digest, Vol 109, Issue 14
Annotation lumi Annotation lumi
13.7 years ago Pan Du ▴ 440
0
votes
0
replies
2.1k
views
reading with lumi
Preprocessing PROcess lumi methylumi Preprocessing PROcess lumi methylumi
13.8 years ago Tim Triche ★ 4.2k
0
votes
0
replies
1.3k
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reading with lumi
lumi lumi
13.8 years ago Ed Siefker ▴ 230
0
votes
10
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1.8k
views
warning in lumi
Proteomics lumi Proteomics lumi
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 110
0
votes
1
reply
2.6k
views
Estimating fold change from limma 'log2FC' using lumi
Microarray Normalization limma lumi Microarray Normalization limma lumi
updated 13.8 years ago by ▴ 30 • written 13.8 years ago by 53k
0
votes
0
replies
1.7k
views
Estimating fold change from limma 'log2FC' using lumi vst instead of log2 transformation?
Microarray qPCR Normalization limma lumi Microarray qPCR Normalization limma lumi
13.8 years ago Ross ▴ 30
0
votes
0
replies
1.6k
views
lumi and 450k control probe files
probe PROcess lumi probe PROcess lumi
13.9 years ago Oliver Hofmann ▴ 50
0
votes
0
replies
728
views
Median/Quantile values table
lumi lumi
14.0 years ago Guest User ★ 13k
0
votes
0
replies
1.3k
views
lumiR Does Not Create lumi Batch
Annotation lumi Annotation lumi
14.0 years ago Sean Davis 21k
244 results • Page 2 of 5
Recent ...
Replies
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.
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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