Questions tagged [microarray]

questions involving microarray analysis (e.g. Illumina BeadChip, Affymetrix GeneChip)

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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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1 answer
57 views

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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2 answers
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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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2 answers
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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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Why there is extra probeID in microarry Raw data (CEL) as compare to data in Series Matrix File & SOFT formatted family file?

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1 answer
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Calculating mean accross rows with repeated entries in R

I have this expression matrix ...
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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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1 answer
43 views

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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1 answer
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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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-1 votes
1 answer
100 views

R error: could not find function "pathwayAnalysis"

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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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1 answer
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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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228 views

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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2 answers
48 views

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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2 votes
1 answer
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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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2 votes
1 answer
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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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7 votes
0 answers
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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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0 votes
1 answer
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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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4 votes
1 answer
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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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1 answer
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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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0 votes
1 answer
345 views

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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2 votes
1 answer
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coexnet package for network co-expression analysis, is looking for a filelist.txt that doesn't exist

On my way to create a co-expression matrix for a microarray experiment, using the coexnet package I had to use a function called ...
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6 votes
1 answer
134 views

Classification (supervised learning) of expression data on pathway level

I was wondering if there is any way to apply classification algorithms (e.g random forest) on microarray data but not using the genes as predictors/features but the pathway they belong to. The thing ...
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2 votes
1 answer
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How hard is it to clean and QC gene expression microarray data?

I am a PhD student working on developing ideas for my dissertation papers. One of my planned papers will be working with some (human) gene expression data. I have had a class on working with gene ...
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5 votes
1 answer
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Pathifier bioconductor package recommends to use technical noise for an argument. How to determine it?

I'm running the pathifier approach against C2 pathway curated database for a specific microarray dataset. As I was reading the documentation of the pathifier, in order to configure it properly for my ...
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3 votes
1 answer
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Integration of different microarray dataset to run GSEA

I'm planning to run a GSE Analysis on some microarray datasets. Until now what I have done is to pre-processed them using frma algorithm. The reason I chose frma instead of gcrma or rma is that I ...
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3 votes
1 answer
217 views

Interpreting large z scores from microarray data

I have microarray z scores for gene set enriched (GSE) pathways that range approximately from -3 to 14. I understand that an absolute value of 1.96 has a p-value = .05 and significant for our purposes....
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4 votes
2 answers
841 views

Normalizing microarray data for clustering heat map

I wanted to generate a clustering heat map for the microarray data. This is the first time I'm working on Microarray data. I read some tutorials but have few doubts. I'm using microarray (Affymetrix ...
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2 votes
1 answer
40 views

Simple Affy Differential Expression

I think I have a fairly easy-to-solve problem. I have an expression table generated from an Affy set. It has one row of gene names (already symbols) and then 180 sample rows. 181 rows total. So I ...
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3 votes
1 answer
192 views

error in heatmap using R

I am learning about generating heatmaps using R. For this example I am using randomly generated data to test the process, but I encountered what appears to be an error or perhaps there is something am ...
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4 votes
1 answer
132 views

Standard Cutoff for Moderated T-statistics

I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma. Is there any standard practice for where to cut off that value? For log2 fold change I ...
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