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Questions tagged [microarray]

A chip-based assay that allows parallel detection of thousands of samples, such as DNA, at once.

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Limma - Voom function for microarray data

I am wondering if anyone can have a look at the voom plot I got below and let me know if this is indicative of an issue with my design? I understand that it should be more of a J-shape rather than a ...
Sachin Rahul's user avatar
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Why do microarrays require a priori knowledge of the genome?

Reading this paper they said this: Contemporary microarrays emerged in the wake of genome sequencing projects for one obvious reason: arrays require a priori knowledge of the query genome Why do you ...
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Why do genes, encoding the same proteins and in the same conditions, have different expression?

Is it possible that two genes, which come from two different cell cultures and which encodes the same protein, produces different quantity of mRNA? If yes, why? My question comes from the fact that I ...
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Quantifying Gene Expression

I have found that many studies use the mRNA concentration as a “proxy” for protein activity because there should be correlation between mRNA levels and proteins expression levels. How is protein ...
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Why are there different gene expressions that are refered to the same gene in microarray experiments results?

I am studying gene expression profiling considering a dataset available on NCBI website. I do not understand the following: why are there some genes that have different profile and different ID ...
Manuela's user avatar
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Microarray experiment validation meaning

I have a quick question: what does microarray experiment validation mean ? I was reading a paper in which they say that the data of the experiment show that the 3 genes radB, dp1 and dp2 are co-...
Manuela's user avatar
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Why do we use cRNA instead of initial extracted RNA in the microarray technique?

I am recapping for the exam in transcriptomics and stumbled into a question about microarray. So, our regular workflow is to extract RNA from cells generate cDNA from the initial RNA using reverse ...
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Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
mindlessgreen's user avatar
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Preprocessing microarray data to detect increased male expression variance due to dosage compensation?

I am currently working with a dataset from a large microarray experiment where one of the aims is to look for evidence of the predicted doubling of variance in expression on the X chromosome in ...
neongolden's user avatar
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Does PCR amplification affect microarray or DNA biosensor results?

I've noticed that PCR amplification is commonly done before analyzing the DNA sample with microarrays or biosensors. However, won't amplification biases or errors mess up the gene expression profile ...
E. Tsai's user avatar
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In microarray normalization, why is the normalization factor this?

I am working on analysis of a huge number of microarray files. I was trying to understand the need for normalization in microarray data and was going through this paper by John Quackenbush(2002). In ...
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Microarray with n channels

Recently we've been learning about Microarrays, and the typical method seems to be to run a two channel microarray where your RNA from each cell is labelled with a different fluorescent marker, and ...
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How do I score differential activity of cellular pathways in microarray data (not enrichment)?

I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset. The goal is to ...
user28560's user avatar
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How to determine continental ancestry group (race) with transcriptome data obtained with RNA microarray?

Say I have a whole genome expression data (transcriptome) for some sampled human tissue. Is this data sufficient to find out the continental ancestry group of a donor?
Sashko Lykhenko's user avatar
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Are the human placenta chorionic villi and villous tree the synonyms?

Are the human placental chorionic villi and the villous tree the synonyms? Or, if not, can I say that these tissues would have practically the same gene expression profile in an RNA microarray ...
Sashko Lykhenko's user avatar
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What do the intervals between groups of arrays in microarray gene expression data images mean?

This can be a dummy question, but I am not familiar with microarray experiments at all. In this image, what does each of 16 big squares mean, and what are the black intervals between them are? I know ...
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Where do I find standard tissue and cell names?

I am developing specialized database on some desease microarray experiments. The initial data is retreived from NCBI and ArrayExpress databases. The problem is that sample attributes sometimes specify ...
Sashko Lykhenko's user avatar
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Is the technology "identitas v1 forensics chip" related to microarray technology?

Available resource but difficult for me to make scence Relation about crime scene and identitas v1 forensics chip Is the technology "identitas v1 forensics chip" related to microarray technology? ...
Snake's user avatar
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Validation by PCR of a lowly expressed gene in microarray

I am interested in validating the precence of a gene (FETUB) whose expression is in the lower quartile of the microarray (see figure in link). https://drive.google.com/open?id=...
Sergio.pv's user avatar
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How many co-expressed genes would be expected in a tissue?

I am working with gene expression microarrays of tumor tissues and I want to use a program to find the clusters of co-expressed genes in order to know if some particular genes are co-expressed with ...
Fernando's user avatar
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What is the most appropriate way to normalize gene expression data?

This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for ...
Fernando's user avatar
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How can microarrays be used to quantitatively determine level of gene expression?

This is probably a stupid question because I don't fully understand how microarray experiments work. I'm trying to understand how microarrays work but I'm confused about something which I can't seem ...
liyuan's user avatar
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What is the aqueous solution for DNA immobilization?

This paper Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips Which is talking about how the electric field improve the DNA immobilization process. ...
Chean Lee's user avatar
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Walkthrough Illumina Genotyping

I would love help outlining a basic walkthrough of the wet-lab techniques for processing blood samples from patients, all the way to loading a BeadChip, to the part just before Next Generation ...
lrthistlethwaite's user avatar
5 votes
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What is meant by "the degree to which a gene is expressed" in an individual?

Here is an excerpt from a text that I was reading, Here is an example of microarray data. The idea is to take a group of different individuals and for each of them, you measure how much they do ...
Solace's user avatar
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What do HG and NA mean in Geuvadis project RNAseq sample labels?

I'm looking at RNASeq Data from Geuvadis website e.g. the file GD660.GeneQuantRPKM.txt.gz. The samples are labeled by e.g. HG00105.1.M_120209_7 or NA20812.2.M_111216_6 What do HG and NA mean? Are ...
Machine's user avatar
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where can I find microarray images?

I have investigated some of the links to known microarray databases, such as arrayTrack, omnibus (NCBI), TCGA. I find that when trying to get microarray images I either get an exotic file format (such ...
hotGopher's user avatar
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1 answer
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Comparison of gene expression time series in vitro and in vivo

I have to analyse two datasets consisting of time-series measurements of gene expression. One set are in vivo data from the expression profiles obtained between a few days before birth to several days ...
Marco's user avatar
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Oscillatory electrical system using a chain of neurons

Many daily activities that we perform are result of inbuilt oscillatory circuits in our body. For example walking, breathing, heart beat, blinking, etc. The coding and decoding of stored memory also ...
9Heads's user avatar
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1 answer
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Genes-of-interest analysis between organisms

I am interested in identifying the differential expression between several genes-of-interest of different organisms. I am trying to assess the benefits of RNA sequencing over microarrays. Both ...
Tomas Scheitel's user avatar
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177 views

What software/approach to use to build a graph based on microarray gene expression correlation?

What software to use to build a graph based on microarray gene expression mutual correlation? I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more ...
VassiaAlk's user avatar
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How to retrieve full gene names list and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any)?

How to retrieve full gene names and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any other software or language)? Is it possible vice versa: having full gene ...
VassiaAlk's user avatar
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1 answer
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What to do if microarray t-test, ANOVA, SAM and LImma show various selected significant genes?

Need advice: how to approach discrepancy in differential microarray gene expression test results: what to do if ANOVA, ttest, SAM and Limma procedures show different results and especially more ...
VassiaAlk's user avatar
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1 answer
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genomatix software linux install [closed]

I have installed the genomatix software which is a jar file the name is InstallChipInspector21.jar.But now I really don;t know how do I start it ,can any one suggest me a method??
krushna's user avatar
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How to automate this custom gene expression microarray chip?

I have 16 gene sequences that I am interested in their detection in clinical samples. I already measured their RNA levels by using RT-qPCR technique and their benefit has already been proven to help ...
doctorate's user avatar
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1 answer
142 views

What makes certain obligate anaerobes viable in fermentation starter cultures?

If Propionibacterium are obligate anaerobes (to wit, poisoned by oxygen), what makes 'Dairy' or classical propionibacteria (e.g. P. shermanii, P. jensenii, P. acidicpropionici, et al) viable in ...
Wilhelm's user avatar
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1 answer
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Reusable microarray chips

Microarray chips allow us to conduct many expression experiments in parallel to each other but they can be used only once as far as i know. Are there reusable microarray chips? Have people ever tried ...
ecagl's user avatar
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Gene perturbation, what is it used for, explain to computer scientists? [closed]

I am trying to build a gene regulation network, and I need some basic knowledge of it. So, in gene research, we perturb genes. Such as knock down them? Can people tell 2 or 3 experiment methods to ...
GeekCat's user avatar
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1 answer
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What information do microarray image convey?

OK I have read that a cell generates 4 kinds of digital (to be precise discrete) data namely DNA, RNA, Protein (sequences that can be encoded as string sequences of nucleotides/ amino acids) and micro ...
dexterdev's user avatar
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Single channel micro arrays

What does single channel microarray mean? When is it used? Thank you for your case in advance.
user6175's user avatar
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Are there any differences between qRT-PCR and GEO (microarray data from NCBI) regarding dealing with internal control genes?

As we know, when we do qRT-PCR, the two most commonly used methods are absolute quantification and relative quantification, both the methods are involved in dealing with normalization of house-keeping ...
peter cai's user avatar
2 votes
1 answer
819 views

Microarray gene expression matrix format

After scanning the microarray chip we get RAW data with different formats depending on the type of microarray used. However, these RAW data files can be normalized and processed to generate gene ...
Lamia's user avatar
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16 votes
1 answer
350 views

At which step should I apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)

What is the best practice when preprocessing microarray data using a detection filter (on scanner p-value)? Suppose I have a microarray dataset that I have to normalize with Loess and correct with ...
gc5's user avatar
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5 votes
1 answer
407 views

Microarray data and analysis tools

Microarray has various uses, and to analyse the data a main function classification is used. There are many methods used to classify the data but what are the best and most frequently used methods? ...
Lamia's user avatar
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