Showing : beadarraysnp • reset
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CRLMM on Illumina Human1Mv1_C chips
crlmm illumina beadarraysnp
updated 6.6 years ago by ▴ 1000 • written 6.6 years ago by ▴ 30
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How to normalize Illumina bead-level data ?
SNP Normalization GO PROcess beadarraySNP SNP Normalization GO PROcess beadarraySNP
11.4 years ago Jonas Mandel ▴ 10
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BeadarraySNP/read.SnpSetIllumina
beadarraySNP beadarraySNP
12.2 years ago Boris Umylny ▴ 120
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758
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Simple beadarraySNP analysis
SNP Normalization Cancer Colon PROcess beadarraySNP copynumber SNP Normalization Cancer
12.3 years ago Dmitri Mouradov ▴ 20
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1
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894
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Problem reading data with beadarray package
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 13.9 years ago by ▴ 460 • written 13.9 years ago by ▴ 10
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Pulling significant gene ids from beadarray data
Biobase annotate affy affyio beadarray quantsmooth beadarraySNP lumi Biobase annotate
14.1 years ago Johnstone, Alice ▴ 410
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1
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749
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beadarray - combing
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 14.1 years ago by ▴ 320 • written 14.1 years ago by ▴ 270
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1
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760
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ControlID Qcinfo slot in Illumina beadarray summary data?
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 14.1 years ago by ▴ 320 • written 14.1 years ago by ▴ 410
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3
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1.0k
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beadarray package: problem with bead level data
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 14.2 years ago by ▴ 40 • written 14.2 years ago by ▴ 270
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1
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750
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beadarray readIllumina suggestions
Microarray Annotation geneplotter affy affyio beadarray quantsmooth beadarraySNP affy
updated 14.3 years ago by ▴ 460 • written 14.3 years ago by ▴ 10
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Comment: Extracting normalized counts in MEDIPS by Lukas ▴ 10
Hi Ishepard, I am glad to hear that the quantile normalized values give you reasonable visualizations. The TMM normalization happens withi…
Comment: Extracting normalized counts in MEDIPS by lshepard ▴ 40
Hi Lukas, thank you for the quick reply! Understood on the warning. Makes sense now. Regarding visualization - simply put, yes on a "per …
Comment: Extracting normalized counts in MEDIPS by Lukas ▴ 10
Hi, Thanks for your inquiry! >When quantile normalization are selected: >Results table count have quantile normalized values, which is w…
Comment: Extracting normalized counts in MEDIPS by lshepard ▴ 40
Hello Lukas. Thank you for the reply. After coming back to this after a while and normalizing by quantile it seems like the counts are actu…
Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
If this is taking too long, you can run it on a subsample (e.g. hundreds of samples) to identify parameters for the VST, and then apply it …
Votes
Comment: Extracting normalized counts in MEDIPS
Comment: "full model matrix is less than full rank"
A: Extracting normalized counts in MEDIPS
Answer: "full model matrix is less than full rank"
Comment: Unique GPos taking into account mcols
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