Questions tagged [microarray]
questions involving microarray analysis (e.g. Illumina BeadChip, Affymetrix GeneChip)
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Does using a microarray chip that matches the chip used in training lead to higher explained variance of a polygenic score?
I'm trying to replicate an existing polygenic score (i.e. test the accuracy in a new sample), and want to know if matching the original study's microarray chip will improve the accuracy (that is, ...
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Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated
I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested ...
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Does pooled sample genotyping microarray analysis exist?
I want to genotype samples in small batches with a common microarray (e.g., the GSA). However, the cost is very high for small batches.
With a higher sample throughput/volume, per sample cost becomes ...
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Does phasing improve imputation quality?
If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.
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Adding BAF and Log2 ratio to VCF file
I have access to pre-processed VCF files from a genetic dataset, and am trying to use the MoChA tool to calculate mosaic chromosomal alterations in this dataset. However, MoChA requires BAF and ...
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illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion [closed]
This question has been cross-posted on Biostars but has not received any answers yet, so I'm posting it here. I'll update here if it gets answered there.
I have downloaded a miRNA expression dataset ...
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DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values
This question was also asked on Biostars
I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized ...
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Should I compensate for two clusters of samples in microarray by hierarchical clustering and MDS?
I seem to have two groups of samples based on hierarchical clustering as well as MDS plot analysis using the sample label from the tree cut of the hierarchial clustering. I am analyzing microarray ...
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Allele effects by parental-origin estimated from genotyping array data
We are dealing with relatively large family data (> 1,000 trios) with genotyping array data.
We would like to see the allele effects on children separately of mothers, fathers, and children, as in ...
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Handling of sex chromosomes in male when computing CNV copy ratio
Reading from CNVkit documentation, Mathworks documentation, Bionano documentation, for CNV calling, it seems that the common practice for array is to compute the linear copy ratio by normalizing ...
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Cromwell - controlling core/mem usage, and CallCaching, while running locally?
I'm sitting on a mountain of microarray (.idat files) data, and have been tasked to analyze it. I chose the MoChA pipeline, developed by the Broad Institute. It runs through Cromwell, of which I know ...
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Creating msk file for Illumina Array Analysis CLI Copy number train
recently I'm researching on how to detect CNV from Illumina microarray data. I found that Illumina has Array Analysis CLI software for this task, and I need to train the CN model myself, since the ...
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open source tools for CNV analysis from illumina SNP array
What are the best open source tools to analyse copy number variation using Illumina SNP array data...preferably R based tools, but open to other languages as well.
I'm working with leukemia sample and ...
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What is the correct order of flooring-normalization-batch correction for microarrays?
This question was also asked on Biostars
I am trying to learn and understand the correct order of data processing steps for microarrays.
I have data which already was analyzed by a researcher using ...
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What could explain the difference in RNA-seq and Microarray expression levels?
What are some possible reasons why some trends observed in Microarray expression levels is not observed in RNA-seq. Example the difference between 2 cell types for a gene of interest show major ...
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How to compare across Microarray datasets for a gene in Mice?
How does one go about comparing expression levels of one gene across multiple microarray datasets pulled from different experiments/papers in mice? In my example, I've downloaded the expression levels ...
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Accessing expression data in an ExpressionSet
I used rma from the oligo package to normalize CEL files, returning an object of class ExpressionSet. How do I access the actual ...
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Different results in differential expression analysis of microarray data
I am performing differential gene expression analysis to microarray data for type 2 diabetes donors and nondiabetic donors. When I run the code I get some different results in each time (about 50 or ...
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P value recalculation from multiple analysis (Transcriptomics)
I've done a differential expression analysis with transcriptomic information (microarrays and RNAseq) from different datasets by applying for some of them t-test and for the rest Wald-test. I've got ...
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Bioconductor, genefilter() returns NULL dimensions, is my filtering process wrong?
I'm using R and bioconductor in order to conduct some gene analysis on an Affymetrix dataset (GSE173360) but I'm having trouble at filtering genes. I'm trying to create a dataset called small.eset by ...
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multi--platform GEO analysis based in expression of single gene
This question has also been asked on Biostars
I have a challenge in analyzing GSE34941( It has 4 platforms) according to the expression of a specific gene in R. First, which is the best way to group ...
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How to tell which channel is the reference channel in two channel (red green) array data?
I'm sorry if this is a stupid question - I have not analysed two channel array data before.
I have a GenePix data file, which does not seem to indicate which channel (red or green) is used as ...
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How to check if a given gene is expressed in a group of microarray samples if I do not have control group to compare with?
I have a microarray gene expression dataset consisting of placenta samples. I want to check whether these placenta samples are mixed with maternal decidua tissue. I have marker genes for decidua ...
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Meta-analysis in R [closed]
I am completely new to meta-analysis and am a bit lost on how to proceed.
I have two biomarker datasets; each one is using a different microarray platform. I have the protein names, the concentration ...
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Why is Mann-Whitney U-Test over an ExpressionSet yielding different results than original paper
I am trying to replicate the results of this paper roughly guided by this pipeline.
Basically, we are trying to detect a differential expression between mesenchymal and epithelial cells under ...
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Time for running ADMIXTURE analysis
I am trying to run the ADMIXTURE software for the first time to analyse the structure of an in-house dataset of samples comparing to 1000 genomes project ancestral populations. I am trying to ...
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Combining several different affymetrix expression microarray experiments for further MDS analysis
Assume that I have three different Affymetrix microarray experiments, 2x U133 (from 2015 and 2017) and 1xU133 Plus 2.0 (2019). Each array contains several different samples, some of them are common ...
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How can I collapse probes to single value per gene using GEOquery?
I have extracted microarray gene expression data from GEO using the GEOquery package in R. There are multiple probes per gene. Is there a way to select the best ...
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What RNA-Seq expression value would be closest to Microarray equivalent?
I know this question may seem strange.
I'm using Spearman correlation between gene expression profiles for various reasons (I won't go into details here). As a result, I often compare RNA-Seq and ...
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Gene Ontology Specific Fold Changes
I am currently doing a project involving gene rank correlations. How we rank our genes is based on the absolute values of the log2 fold change. I.e. a gene which is doubled with respect to the ...
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How to perform DE analysis for each sample
I am new to R and biocondunctor. I have the normalized expression values for 20 samples for a disease and for 10 controls. I wanted to get the differential expressed values for each sample with all 10 ...
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How can extract the list of genes name from the raw data in GEO?
The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R?
I would ...
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How can I correctly get 3D scatter plot for micro-array pheno data in R [updated]?
I intend to see data points distribution (each reows) within labeled groups (different batchs such as 1,2,3, and so on) in 3D scatter plot, because I want to see the distribution of the data points ...
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Any way to filter out highly correlated genes with limma linear model?
I have Affymetrix gene level expression matrix (genes in the rows and sample ID on the columns), and I have annotation data of microarray experiment observation where sample ID in the rows and ...
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Any way to quantify the variation of genes that expressed in Affymetrix expression data?
am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) for my downstream analysis. Here ...
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How can I convert Affymetrix microarray data to bedgraph format?
I've previously asked a different question about the ChIP-chip microarray data that I'm working on. I'm new to this so I'm sorry for asking here again.
I have .CEL files and I'm using the Affy ...
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Extracting expression data in r from GEO and got a S4 object
I want to open the expression data GSE9838 dataset from GEO using GEOquery R package.
gset <- getGEO(filename="GSE9838_family.soft.gz")
The result of this ...
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Differentially methylated position analysis in a related sample?
I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is:
...
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Affymetrix tags (same ID's) present in different places of the genome
could you explain me how to interpret such situation?
Same tag aligned in several distint places, near different genes...
Is the annotation able to distuinguish such 'same' tags, during DGE analysis?
...
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Where can I find .cdf files for Affymetrix ChIP-chip data analysis?
I am analysing microarray ChIP data generated several years ago. I want to use the affy package for R. However, in order to load the CEL files and proceed with the analysis, I need the pombe ...
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161
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Combat for multiplatform batch correction
I have been looking ways to use data from various micro-array platform such as agilient, rosetta/merk. Some of the established method I came across is combat, but I'm not sure if it can be done for ...
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Question about the dots on Quartile groups in boxplot
I have Microarray Normalized Expression data for a specific Gene. It looks like below in a dataframe B
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Gene not found in Affymetrix expression profiles
I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249.
I downloaded the following file in ...
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What are some good sources of 3rd order gene expression data
I need good sources of gene expression data in the form of 3rd order tensors. Typically the commonly available datasets are in the form of a matrix, for instance, $sample \times gene$ or $gene \times ...
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Hierarchical models with limma?
I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
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How to calculate call detection values in microarray datase if .cel file unavailable
I would like to do a differential gene expression analysis on a microarray data. From the literature, I understood, call detection (Present, Absent, Marginal) has to be done to minimize false ...
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What is a standard approach to binarize microarray gene expression data?
I am using gene expression data from a microarray dataset for the purpose of learning the network structure of genes in the dataset.
Now to do this I need to binarize my data, i.e convert the data ...
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