Skip to main content

Questions tagged [microarray]

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

Filter by
Sorted by
Tagged with
0 votes
1 answer
15 views

Inconsistent microarray expression levels after normalizing with log2

I know it is necessary to normalize the GEO microassay data before analysing. Howerver, after using log2 to normalize the data and checking with boxplot, I found the data is still not align in the ...
Bioinfotec's user avatar
1 vote
1 answer
18 views

When analysing microarray data, is it need to do normalization and standardization both?

When we do differential expression analysis, it is common to normalize the data using a log transform: exprs(gse) <- log2(exprs(gse)) This ensures that the ...
Bioinfotec's user avatar
0 votes
0 answers
10 views

Practical challenges for microarray analysis and single cell

currently, I am learning single-cell sequencing and microarray analysis. I am searching for somewhere (or any alternative way)to practice and get hands-on with these techniques. please help me with ...
Hossein Azadinejad's user avatar
2 votes
0 answers
122 views

GSEA vs GSVA: Pros and cons of each method

Trying to understand when GSEA is more appropriate than GSVA and vice versa. I have seen cases when running GSEA and GSVA on the same task - compare enrichment of a geneset between two groups - gives ...
Tomas Bencomo's user avatar
2 votes
1 answer
28 views

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, ...
BigMistake's user avatar
0 votes
0 answers
29 views

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 ...
shaimaa Hassan's user avatar
1 vote
0 answers
41 views

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 ...
BigMistake's user avatar
0 votes
1 answer
52 views

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.
BigMistake's user avatar
0 votes
0 answers
14 views

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 ...
Akshaj Darbar's user avatar
2 votes
0 answers
46 views

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 ...
accibio's user avatar
  • 145
1 vote
1 answer
175 views

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 ...
accibio's user avatar
  • 145
2 votes
1 answer
45 views

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 ...
siddhartha das's user avatar
1 vote
1 answer
90 views

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 ...
PenguinPartyH0's user avatar
1 vote
0 answers
23 views

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 ...
gc5's user avatar
  • 1,783
1 vote
0 answers
30 views

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 ...
Joel's user avatar
  • 11
1 vote
0 answers
38 views

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 ...
Thanh Nguyen's user avatar
2 votes
0 answers
56 views

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 ...
newbiocoder's user avatar
0 votes
1 answer
42 views

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 ...
Sam's user avatar
  • 149
0 votes
2 answers
81 views

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 ...
user305902's user avatar
0 votes
1 answer
53 views

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 ...
user305902's user avatar
1 vote
1 answer
403 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 ...
amin's user avatar
  • 11
0 votes
1 answer
92 views

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 ...
guest's user avatar
  • 1
1 vote
2 answers
30 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 ...
Gero's user avatar
  • 73
1 vote
0 answers
17 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 ...
puredata's user avatar
  • 111
0 votes
1 answer
39 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 ...
amir navidi's user avatar
0 votes
1 answer
18 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 ...
Heather Harrington's user avatar
0 votes
1 answer
58 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 ...
Sashko Lykhenko's user avatar
1 vote
0 answers
61 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 ...
vdu12345's user avatar
0 votes
2 answers
83 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 ...
CSP's user avatar
  • 11
1 vote
1 answer
602 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 ...
Iriel's user avatar
  • 31
1 vote
0 answers
51 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 ...
Adamm's user avatar
  • 206
2 votes
0 answers
271 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 ...
Sylvia Rodriguez's user avatar
0 votes
2 answers
120 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 ...
RoB's user avatar
  • 146
2 votes
0 answers
38 views

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

...
user avatar
-2 votes
1 answer
44 views

Calculating mean accross rows with repeated entries in R

I have this expression matrix ...
Zizogolu's user avatar
  • 2,148
1 vote
0 answers
60 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 ...
Angus Campbell's user avatar
0 votes
1 answer
54 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 ...
Vinay Bharadhwaj's user avatar
1 vote
1 answer
133 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 ...
user4091's user avatar
-1 votes
1 answer
136 views

R error: could not find function "pathwayAnalysis"

...
kcm's user avatar
  • 1,804
1 vote
0 answers
261 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 ...
Jerry07's user avatar
  • 145
2 votes
1 answer
131 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 ...
Jerry07's user avatar
  • 145
1 vote
2 answers
64 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 ...
Jerry07's user avatar
  • 145
1 vote
0 answers
185 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 ...
Min's user avatar
  • 11
1 vote
1 answer
936 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 ...
Qiran's user avatar
  • 11
3 votes
0 answers
266 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: ...
Hayley Sowards's user avatar
0 votes
2 answers
52 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? ...
Adamm's user avatar
  • 206
0 votes
1 answer
331 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 ...
Min's user avatar
  • 11
2 votes
1 answer
167 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 ...
kcm's user avatar
  • 1,804
2 votes
1 answer
269 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 ...
beginner's user avatar
  • 631
7 votes
1 answer
79 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 ...
wrong_path's user avatar