Showing : beadarray • reset
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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
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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
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beadarray: combining swaths for gene expression
beadarray beadarray
13.2 years ago Thomas Kelder ▴ 10
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Beadarray Filtering by Probequality
Annotation beadarray Annotation beadarray
13.2 years ago Mark Dunning ★ 1.1k
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Beadarray Filtering by Probequality
beadarray beadarray
13.3 years ago Guest User ★ 13k
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1
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1.1k
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illuminaHumanv4.db missing keys in last version
beadarray beadarray
updated 13.4 years ago by ★ 7.2k • written 13.4 years ago by ▴ 50
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beadarray package: get error message when using summarize function
Annotation beadarray Annotation beadarray
13.4 years ago bzguan@ucdavis.edu ▴ 30
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importing iScan data into beadarray
PROcess beadarray PROcess beadarray
13.5 years ago Craig Johnson ▴ 20
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2
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1.4k
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question with reading bead summary data into beadarray
beadarray beadarray
updated 13.6 years ago by ★ 1.1k • written 13.6 years ago by ★ 1.3k
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1.6k
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Illumina beadarray analysis with lumi
Normalization Preprocessing probe PROcess beadarray lumi Normalization Preprocessing probe
13.6 years ago Ahmet ZEHIR ▴ 50
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Can beadarray be use to analyze iScan raw data without perBeadFile.txt files?
PROcess beadarray PROcess beadarray
13.6 years ago Mike Smith ★ 6.6k
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1.1k
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Can beadarray be use to analyze iScan raw data without perBeadFile.txt files?
PROcess beadarray PROcess beadarray
updated 13.6 years ago by ★ 6.6k • written 13.6 years ago by ★ 13k
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1.0k
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Fwd: beadarray package: BASH error
beadarray beadarray
updated 13.7 years ago by ▴ 120 • written 13.7 years ago by ★ 8.2k
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1
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772
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beadarray package: BASH error
beadarray beadarray
updated 13.7 years ago by ★ 8.2k • written 13.7 years ago by ★ 13k
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886
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Get negative control probes in lumiBarnes data set
beadarray lumi beadarray lumi
13.7 years ago Guest User ★ 13k
1
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2
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8.3k
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LIMMA - summarization of Illumina probes for same gene
probe affy limma beadarray probe affy limma beadarray
updated 13.7 years ago by ▴ 180 • written 13.7 years ago by 53k
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795
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Need immediate help please-BeadSummaryData
GO beadarray GO beadarray
13.7 years ago Cute Guy ▴ 10
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1.0k
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LIMMA - summarization
beadarray beadarray
13.7 years ago Kripa R ▴ 180
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1
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909
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beadarray vignette has broken code in R2.14.1?
illuminaHumanv2 limma GEOquery beadarray illuminaHumanv2 limma GEOquery beadarray
updated 13.7 years ago by ▴ 20 • written 13.8 years ago by ★ 8.2k
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1
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1.6k
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FrozenRMA how to
Microarray Network hgu133plus2 Biobase PROcess KEGGSOAP beadarray EBImage edgeR frma
updated 13.8 years ago by ▴ 830 • written 13.8 years ago by ▴ 20
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826
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beadarray vignette has broken code in R2.14.1?
illuminaHumanv2 limma GEOquery beadarray illuminaHumanv2 limma GEOquery beadarray
13.8 years ago Henriquez, Nick ▴ 20
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1
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1.1k
views
using beadarray to analyze data from iScan
beadarray beadarray
updated 14.0 years ago by ★ 6.6k • written 14.0 years ago by ▴ 30
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4
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1.5k
views
MA plots for large number of arrays
affy affyPLM beadarray lumi affy affyPLM beadarray lumi
updated 14.1 years ago by ▴ 740 • written 14.1 years ago by ▴ 360
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1
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927
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Beadarray: bead-level data, background intensities
beadarray beadarray
updated 14.3 years ago by ★ 6.6k • written 14.3 years ago by ▴ 20
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707
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beadarray pre-processing - multi-probes per gene
annotate beadarray annotate beadarray
14.4 years ago Laurent David ▴ 10
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1
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1.1k
views
readQC in the beadarray package
beadarray beadarray
updated 14.4 years ago by ★ 1.1k • written 14.4 years ago by ▴ 10
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2
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1.4k
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illumina beadarray GEO files
Microarray beadarray Microarray beadarray
updated 14.5 years ago by ▴ 610 • written 14.5 years ago by ▴ 280
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1
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1.2k
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analyse GSM files form GEO repository
beadarray beadarray
updated 14.5 years ago by 21k • written 14.5 years ago by ▴ 280
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1
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847
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Paired tests using limma and beadarray
Annotation Preprocessing limma beadarray Annotation Preprocessing limma beadarray
14.6 years ago Gordon Smyth 53k
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1
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974
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Paired tests using limma and beadarray
Annotation limma beadarray Annotation limma beadarray
updated 14.6 years ago by 68k • written 14.6 years ago by ▴ 100
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6
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1.8k
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summarized expression values from beadarray versus GenomeStudio
Normalization beadarray Normalization beadarray
updated 14.7 years ago by ★ 1.1k • written 14.7 years ago by ▴ 620
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6
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1.7k
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beadarray: Running BASH for 120 sections
PROcess beadarray PROcess beadarray
updated 14.7 years ago by ★ 6.6k • written 14.7 years ago by ▴ 220
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1
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1.0k
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transfering Illumina Beadarray data from Partek into Bioconductor's beadarray in order to run Limma
Microarray Preprocessing limma beadarray Microarray Preprocessing limma beadarray
updated 14.7 years ago by ★ 3.6k • written 14.7 years ago by ★ 1.1k
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936
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transfering Illumina Beadarray data from Partek into Bioconductor's beadarray in order to run Limma
Microarray beadarray Microarray beadarray
14.7 years ago Gustavo Kijak ▴ 10
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9
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2.5k
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problems with readIllumina() for many BeadChips
beadarray beadarray
updated 14.8 years ago by ★ 6.6k • written 14.8 years ago by ▴ 620
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2
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1.2k
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Beadarray SAMExample tutorial: readIllumina problem
beadarray beadarray
14.8 years ago Sarah Allen ▴ 30
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1.2k
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beadarray: Error when reading control probe profile with readBeadSummaryData
probe beadarray probe beadarray
updated 14.9 years ago by ★ 1.1k • written 14.9 years ago by ▴ 100
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beadarray: how to create BeadStudio output after createBeadSummaryData
PROcess beadarray ArrayExpress PROcess beadarray ArrayExpress
14.9 years ago Cei Abreu-Goodger ▴ 830
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3
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1.4k
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Beadarray - problem with BSData object created using 'summarize'
beadarray beadarray
updated 14.9 years ago by ★ 1.1k • written 14.9 years ago by ▴ 20
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3
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1.4k
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About package beadarray
Normalization PROcess beadarray Normalization PROcess beadarray
updated 14.9 years ago by ★ 1.1k • written 14.9 years ago by ▴ 60
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1
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1.6k
views
crlmm - Infinium iSelect HD Custom Genotyping
SNP beadarray crlmm SNP beadarray crlmm
updated 14.9 years ago by ▴ 1000 • written 15.0 years ago by ▴ 20
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1
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1.4k
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problems with readIllumina()
beadarray beadarray
updated 15.0 years ago by ★ 1.1k • written 15.0 years ago by ▴ 620
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1
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751
views
About package beadarray
beadarray beadarray
updated 15.0 years ago by ★ 1.1k • written 15.0 years ago by ▴ 20
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4
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1.4k
views
combineBeadLevelLists() in Bioconductor 2.8 beadarray
beadarray beadarray
updated 15.0 years ago by ★ 1.1k • written 15.0 years ago by ▴ 650
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1
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1.0k
views
problem with beadarray package 2.0
beadarray beadarray
updated 15.0 years ago by ★ 4.2k • written 15.0 years ago by ▴ 10
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1
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1.1k
views
beadarray, bash, hulk, excludeBrihtBeadNeighbors, et al -- how to use practically?
Cancer beadarray EBImage Cancer beadarray EBImage
updated 15.0 years ago by ▴ 60 • written 15.1 years ago by ★ 1.1k
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0
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870
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beadarray locs files
beadarray beadarray
15.0 years ago Alex Gutteridge ▴ 650
0
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1
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927
views
beadarray without qcFile
beadarray beadarray
updated 15.1 years ago by ★ 1.1k • written 15.1 years ago by ▴ 650
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2
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1.5k
views
decideTests limitation to certain lfc and p values not working
Category beadarray Category beadarray
updated 15.1 years ago by ▴ 650 • written 15.1 years ago by ▴ 100
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0
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833
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Error in imageplot with .locs files
beadarray beadarray
15.1 years ago Mike Smith ★ 6.6k
181 results • Page 2 of 4
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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.
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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