Questions tagged [microarray]

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

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30 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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22 views

Different results in Differential Expression analysis of Microarray Data

I'm new to R, so be patient with me. 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 ...
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2answers
17 views

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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14 views

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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9 views

Microarray: Build annotation for HT MG430PM affymetrix

I'm new to affymetrix analysis and have been following several tutorial to analyze microarrays. I have to analyze a specific microarray (GSE33948 - GPL11180) that used the HT MG430PM array plate, but ...
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27 views

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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1answer
15 views

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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22 views

How to merge several microarray-based gene expression datasets while not excluding genes that are not present in all datasets?

In integrative gene expression analysis when two expression matrices from different datasets are merged together, they are usually merged by common genes in both expression matrices while all other ...
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1answer
50 views

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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22 views

? What meaning do positive and negative values have in the centroid plot for genes?

I was working with a dataset containing genes. The central plot of the model after using "shrunken centroid" is like the following picture: I noticed that they can all be negative ...
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48 views

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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2answers
60 views

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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1answer
147 views

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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49 views

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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93 views

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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2answers
79 views

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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1answer
40 views

Calculating mean accross rows with repeated entries in R

I have this expression matrix ...
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24 views

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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1answer
41 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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39 views

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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83 views

R error: could not find function "pathwayAnalysis"

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126 views

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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62 views

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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2answers
52 views

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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108 views

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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1answer
422 views

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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204 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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2answers
47 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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1answer
219 views

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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1answer
96 views

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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1answer
184 views

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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53 views

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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1answer
30 views

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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1answer
671 views

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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1answer
93 views

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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1answer
304 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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1answer
67 views

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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1answer
123 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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1answer
106 views

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 ...
4
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1answer
61 views

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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1answer
87 views

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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1answer
202 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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2answers
797 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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1answer
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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1answer
181 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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1answer
128 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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1answer
60 views

Differences between NetAffx Hg-U133 Plus 2.0 Annotation file versions

From what I was able to observe, the annotation files (CSV) for NetAffx Hg-U133 Plus 2.0 is updated regularly. However, from glancing at the CSV files (NA35: 2015 & NA22: 2007), I can't seem to ...
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1answer
958 views

Using the t-SNE algorithm on microarray data + an error bonus

I'm trying to use the t-SNE algorithm on some microarrays data. More specifically my data frame has 18600 columns with genes (features) and 72 rows with conditions with replicates ( 10xWt , 10xTg , ...
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1answer
6k views

Extracting expression data from GSE dataset downloaded from GEO

I have downloaded GSE16146 dataset from GEO using GEOquery R package. I would like to extract "Data table" from downloaded GSE16146. ...