Tag: RMA

Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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Repair or Rebuilt Van Dorn/Demag 330029 SEQ Sequencer Board

Repair Price: Send item for an expert evaluation Request Evaluation CSL Part Number: 34027 Category: Control Board Manufacturer: Van Dorn/Demag Manufacturer…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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RMA on different disease labels

RMA on different disease labels 0 I’m working with HGU133Plus2 datasets, and I’m determining the best normalization procedures. RMA seems to be the standard in literature, however some papers have been opting away from global normalization procedures: www.nature.com/articles/s41598-020-72664-6 ieeexplore.ieee.org/document/6999142 I’m not familiar with how the statistics with RMA works. So…

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Reproductive Medicine Associates of New York Presents Innovative Research at ASRM’s 77th Annual Meeting

RMA of New York leads the way with ground-breaking innovative genomics and artificial intelligence research to improve patient care and IVF success rates Published: Oct. 19, 2021 at 9:00 AM MDT|Updated: 4 hours ago BALTIMORE, Md., Oct. 19, 2021 /PRNewswire/ — Physicians and scientists at Reproductive Medicine Associates of New York…

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Reading microarray data from the Gene Expression Omnibus

Hi Caitlin, For this study, the uploaded data is normalised via GC-RMA, but is not log [base 2] (log2) transformed. To retrieve it, you need to do: library(GEOquery) gset <- getGEO(‘GSE12657’, GSEMatrix = TRUE, getGPL= FALSE) if (length(gset) > 1) idx <- grep(‘GPL8300’, attr(gset, ‘names’)) else idx <- 1 gset…

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Network plot from expression data in R using igraph

[last update: January 27, 2020] igraph allows you to generate a graph object and search for communities (clusters or modules) of related nodes / vertices. igraph is utilised in the R implementation of the popular Phenograph cluster and community detection algorithm (used in scRNA-seq and mass cytometry), and also in…

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GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip)

Sample code for GSE79404 #!/usr/bin/Rscript # general config baseDir <- ‘GSE79404/’ bgxfile <- ‘Annot/HumanHT-12_V4_0_R2_15002873_B.bgx’ targetsfile <- ‘targets.txt’ setwd(baseDir) options(scipen = 99) require(limma) require(RColorBrewer) require(PCAtools) # read in the data and convert the data to an EListRaw object, which is a data object for single channel data x <- read.table(paste0(baseDir, ‘raw/GSE79404_non-normalized.txt’),…

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Bioconductor – xps

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see xps. Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays Bioconductor version: 2.9 The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays,…

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Analysing Microarray Data In Bioconductor

I was thinking about creating a tutorial on how to do a simple microarray analysis in Bioconductor. But, I realized this has already been done quite nicely at the Bioinformatics Knowledgeblog. Their first tutorial on the subject covers installation of necessary packages, downloading of cel files, describing the experiment, loading…

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Transcriptome Analysis Console (TAC) VS Oligo package in bioconductor

Transcriptome Analysis Console (TAC) VS Oligo package in bioconductor 0 I’m a beginner at processing microarray data. I have 114 CEL files (chip: GeneChip™ miRNA 4.0 Array). I tried the following 2 ways to get the signal values and the output is different with no consistent direction. 1.Transcriptome Analysis Console…

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Microarray data normalization

Microarray data normalization 1 Dear all, Sorry for such a basic question, but I got confused. As far as I know, the RMA method implemented in affy package is a standard method for microarray data normalization. Could you let me know if the main code data.rma.norm = rma(raw.data) normalize data…

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Clariom-D array – subsetting probes to known genes prior to normalization

Clariom-D array – subsetting probes to known genes prior to normalization 0 I am analyzing Clariom-D array data using the oligo package in R. I find that the rma normalization step using all probesets works reasonably well (normalized intensity boxplots centered and evenly distributed), but upon filtering the results only…

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Strange difference in the order of probe ID between my matrix from cel and the series matrix the author uploaded

Hi all,I met a very strange error when reading and doing RMA of the raw cel files. When i use the following codes to do the background correction and normalization of GSE18997 (platform GPL570), I found the order of some probe IDs of the final results seems to be different…

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