Talk:DNA microarray

message: Here is a list of terms which are used in the article which should be defined:
*Disease gene" - ambiguous to a layman. Are you talking about genes that cause disease, or the genes of some virus or bacterium?
: Could be either in this case, one is a foreign gene, the other is a mutation 
*reporters" - if this is the same as a "probe", you should say so
: Yes, Reporters is a MIAME compliance term for what is historically a probe
*eukaryotic" - ok, I know what this is, but there should be a link to the topic
*oligonucleotides" - pretty technical for a non-journal article
: See oligonucleotide
*up-regulated" - no clue
: Genes that are upregulated are more highly expressed in a (for example) diseased cell versus a normal cell.
*down-regulated" - still no clue
: Genes that are downregulated are expressed less (lower mRMA levels) in one cell type veruss another
*fluorofores" - ditto
*scanned" - with what? an electron microsope? Seems like a pretty important part of the process to skip.
: Usually a lazer and photomultiplier tube to detect the emitted flourescence
*piezoelectric deposition" - I know what piezoelectric is, but not the process. How about a link?
*60-mer: - no idea
: the length of an oligonucleotide (60 bases in length) --Zven 23:40, 24 September 2006 (UTC)
thread_title: Terms

message: This is a fine edit, to reintroduce British spelling, but the page is in mixed dialect; consider the section header "Standardization".  If an editor is going to insist on usage of one dialect, then that dialect should be used throughout the article and not randomly here and there.  It is difficult to take the editor seriously when a word in the midst of text is pounced upon while a heading contrarily blazes a few lines away. Courtland 04:31, 30 October 2005 (UTC)
thread_title:  About the edit that re-introduced British spelling 

message: I've always understood there being two main types of microarray - oligonucleotide arrays and cDNA arrays.
The oligo arrays have 25bp oligos spotted onto the slide (I think these are Affy chips?) while the cDNA arrays have the cDNA from a single gene on each spot.
Is this correct? It's not made clear by the article in its current form. If it is true, then I think this distinction should be emphasised as it can be quite confusing (I'm confused). Eirinn 11:44, 4 November 2005 (UTC)
thread_title:  Oligos VS cDNA 

message: Someone added a bunch of companies that I am sure exist but don't believe they are important enough to mention here.  I will remove all but the premiere ones like Agilent, Affymetrix etc. unless someone has any objections. --Blacksun 07:42, 18 May 2006 (UTC)
thread_title: List of companies

message: I don't like the way lead is written right now.  The lead should be a clear and concise summary of what microarrays are, how they work, and why they are important.  I am going to attempt to rewrite it to achieve this.  --Blacksun 07:44, 18 May 2006 (UTC)
thread_title: Lead is confusing

message: Shouldn't we talk more about how expression levels are measured and name the common softwares used currently?  It seems to be the missing piece in the article.  I will try to write a bit on it. --Blacksun 07:53, 18 May 2006 (UTC)
thread_title: Measuring expression level

message: The lead talks only about expression arrays, but in later paragraphs it's made clear that there are many types of arrays (SNP, tiling, etc). 
I'd like to generalize the lead a bit more to address the various types of arrays. A DNA microarray doesn't detect gene expression (as stated in the current lead), it detects the hybridization of complementary sequences to the array probes. This can measure various things depending on experimental protocol and array design, including  (but not limited to) mRNA expression levels. gawp 20:26, 7 July 2006 (UTC)
thread_title: Lead talks about expression arrays only

message: Would something on this be appropriate in this article? Aaadddaaammm 08:21, 4 November 2006 (UTC)
replies: text: I am a fan of the fact that when you go diving, red is the first colour to dissapear, a phenomenon that also accurs with these things, but to a less adrenaline pumping level... --Squidonius (talk) 21:24, 7 May 2008 (UTC)
thread_title:  Dye Effect 

message: I made a page for Cy3 and Cy5, but I am aweful at writing and I am new to wiki editing. could someone add a paragragh about dyes used in microarrays? - thanks
I modified the example for the dyes used for the 2-ways microarray. The correct emission for Cy3 is green and for Cy5 red. I removed the references to rhodamine and fluorescein because I think they are are not really used in that context, and are different from Cy3 and Cy5. 
aurel 14:21, 11 September 2007 (UTC)
thread_title:  Dyes used 

message: I've re-instated the two links to Webarray and Arraypipe both of which are online programmes for microarray analysis free of charge that have undergone peer-review in the scientific literature(see: http://www.biomedcentral.com/1471-2105/6/306 and http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215429 ). Please do not remove these links by merely replacing them with a hand wave to the Open Directory Project, which itself is a link jungle and not always reliable. Malljaja 10:17, 3 April 2007 (UTC)
replies: text: I've respectfully removed them again as Wikipedia is not a directory WP:NOT#DIR, even for peer reviewed open source software. You can suggest to create a section in Open Directory Project for "Peer Reviewed Free Open Source Software for DNA Microarray", or you can use the original paper references for these tools somewhere in the text, indicating of course their notability and relevance to this topic, or you can reference a third party comprehensive review of FLOSS microarray tools.  Simply listing them does not indicate notability, and invites spam.  Furtehr, your decision to highlight these particular tools and not others is WP:POV and so needs to be explained in text and supported by references. JetheroTalk 04:48, 12 April 2007 (UTC)

text: I've respectfully removed the 'link-farm' again, since WP:NOT#DIR  These resources are not mentioned in the text, and there is no mention of why these are notable with resepct to 'DNA Microarray'. Since it's obviously an 'invitation' to advertise, I've removed the entire 'software' section this time.  If specific software can be tied to advances or watersheds in DNA Microarray fabrication or analysis, then perhaps they can be included in the text directly?  Or if there is an interesting tid-bit about how the development of these tools were driven by the technology or visa versa? 
 
 == Online microarray data-analysis programs and tools ==
 Several Open Directory Project categories list online microarray data analysis programs and tools:
 * 
 * Cyber-T uses a Bayesian probabilistic framework for microarray data analysis 
 * 
 * 
 * 
 * Bioconductor - open source and open development software project for the analysis and comprehension of genomic data
 * Genevestigator : Web-based database and analysis tool to study gene expression across large sets of tissues, developmental stages, drugs, stimuli, and genetic modifications.
 * GeneCAT (Gene Co-expression Analysis Toolbox): Web-based database of gene expression data and expression analysis tools for Arabidopsis thaliana and barley.  
 * GEPAS: Gene Expression Profile Analysis Suite developed in the Bioinformatics Department of the CIPF in Spain.
 * DAVID bioinformatics: A free online bioinformatics resources provides functional interpretation of large lists of genes derived from genomic studies
 * caCORRECT Chip Artifact Correction: A free online quality control tool for Affymetrix microarrays hosted at  Georgia Tech Biomedical Engineering Department 
 * "spm" is an open source package developed in R for the analysis of gene expression data by means of multivariate projection methods
 
--JetheroTalk 04:16, 13 June 2008 (UTC)
thread_title:  links to online data repositories or microarray analysis programmes 

message: The way the Gene chip technology article stands right now, it just seems like a summary of the microarray article or, at least, one commercial term for microarray, so I figured out would find out the opinion of whether other people think these are the same thing or different?? Ciar 23:16, 5 May 2007 (UTC)
replies: text: I agree. It's a weird article and basically a confusing stub of this one, with a name that seems to refer to the Affymetrix chip but is spelled wrong. I think you should just make it redirect here. Madeleine 00:36, 9 May 2007 (UTC)
replies: text: I agree too. It's just a summary of the main article. Merge it. --LasseFolkersen 20:43, 10 May 2007 (UTC)

text: I went ahead and redirected the gene chip article to here. (NoQuarter 15:40, 29 May 2007 (UTC)
thread_title: Merger of Gene chip technology into DNA microarray

message: Are these considered "DNA microarrays"? - UNSIGNED
I am not that familiar with it, but nanopore is a hypothetical/early experimental sequencing method. An array of pores is not a DNA microarray, but a microchip biosensor-kinda thing. --Squidonius (talk) 12:24, 5 April 2008 (UTC)
thread_title:  no mention of nanopore devices? 

message: The result was no merge into DESTINATION PAGE. -- Squidonius (talk) 15:26, 13 April 2008 (UTC)
thread_title:  Proposed section merges 

message: On the Spotted vs. oligonucleotide arrays, the fact that home made spotted arrays give pourer results is putting it lightly and is actually humourus.
The reason people use spotted arrays is that there is no alternative as they want a custom one. cDNA spotted arrays cost 100-200$ vs 400$ slides + reagents. self printed, 20$ the polylysine coated but you need the library, a cDNA one is about 10k$. with commercial slides you get a nice protocol and proprietary reagents, whereas spotted arrays you have to make the yourself (and there is not a standard one, they all are terrible). the failure rate is so much higher too.
I am complaning here and not fixing it myself because this is not something referenceble to a textbook/article and it probably would be edited out. I am asking that that section be changed --Squidonius (talk) 12:12, 26 February 2008 (UTC)
thread_title:  Sugar coat 

message: this article uses the word colour to describe the two differently "coloured" dyes. In reality when talking about dyes one uses the word "channel", which is much more precise (there is not only the dye but also the laser and filters) and used in the official lingo (not only reguarding flourescence: it is even in photoshop, say, to do a colour overlay) but not socially. furthermore Cy3 and Cy5 when you look at them in solution they are deep blue and purple! Is colour used for ease of comprehension or is it a minor error? 3-channel microarrays also exist (red, blue and UV)--Squidonius (talk) 12:17, 5 April 2008 (UTC)
thread_title:  Channel and Colour 

message: Some pages, such as this one have lots of post, and it requires some work to see what has been answered or acknowledged. therefore I have helped make the  template that can be put above a section allowing one to quickly glimpse what has been answered. If you were waiting for an answer but never got one as the post in somewhere in the middle tag it! please voice any queries or comments in the talk page of and not here.
This article in particular is strange as I think it has reached a critical mass and all overly-long sections are continuously trimmed. I would give it a {{tl|toolong} tag which requests that it be split up a bit and summarised and the new articles explanded. Although it may need a bit of reordering first. Gibson's primer of genome science is a bit messy too, but I think this can be improved a great deal, I have not tagged it so, as it is relatively short.
Cheers --Squidonius (talk) 15:22, 13 April 2008 (UTC)
thread_title: New template for talk pages, expecially the larger ones

message: I am going through this discussion page in order to revamp the article. the problem is I got stuck at fixing the intro:
PROPOSED
A DNA microarray is an arrayed series of microscopic spots of DNAoligonucleotides, called features, where each feauture contains picomoles of a specific unique sequence, such a stretch of a gene sequence.
These molecules are the used as probes) to which only the correct target sequence will hybridise under high-stringency conditions; where the target is the labelled mix of either RNA or DNA to be analysed, in the majority of case with a fluorophore-based detection system.
The probes are bound to a solid surface by covalent attachment to a chemical matrix. The solid surface can either be glass or a silicon chip, in which case they are commonly known as gene,genome chip or colloquially Affy Chip when an Affymetrix chip is used.
DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system.
DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.
ORIGINAL
A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to a chemical matrix. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.
:is it too dense? Thanks, any feedback welcome (even insults)--Squidonius (talk) 18:10, 15 April 2008 (UTC)
replies: text: I changed the lead over as I noticed that a unusual vandalalism was removed, it was not really vandalism but a comment about the bad lead, reguardless of feedback.
I apologise for the large amount of comments I have added, but I think this article is back to shape, now. thanks to all that helped with the making the text more readable --Squidonius (talk) 13:45, 18 April 2008 (UTC)
thread_title: New Opening

message: the exception to the rule that microarrays are fluorescent is with μ-imager from Biomesure (A novel sensitive microarray approach for differential screening using probes labelled with two different radioelements . al, Salin H et. 4, s.l. : Nucleic acid research, 2002, Vol. 30.), but it is not in the text because the machine reads only the area of a coverslip, which in my humble personal opinion I believe is utterly ridicoulus. you can put agilent or 22k cDNA microarrays in a phosphoimager screen with P33 (if you have a reason to do that). --Squidonius (talk) 21:20, 7 May 2008 (UTC)
thread_title: Radioactive microarrays

message: I've re-instated and slightly re-worded the lead according to wiki guidelines found here. As any good lead, it should provide a good summary that will draw the interested reader into the article. As such, it needs to be a little more extensive than a couple of sentences and is already in fairly good shape (and has been for some time, imho)--other sections that still require some real work are those dealing with the stats analyses (problems with multiple testings etc), and making the different technical platforms a little more transparent and confluent. Thanks. Malljaja (talk) 01:31, 10 May 2008 (UTC)
replies: text: Oh, m'kay. I was not aware of that. I concur, it is fine now. This article will be FA one day, so I was starting at the top and eventually get to the bottom (or procrastinating from it). Next... types has a bit too much white (maybe a table like in ncRNA might work). --Squidonius (talk) 10:53, 10 May 2008 (UTC)
thread_title: Lead

message: I'm surprised there isn't a section (or even a mention) of comparative analysis in this article. "comparative analysis" dna yields over 100,000 hits on Google Scholar. Is there another name I don't know? If not, it should definitely worked into this article. Cheers, Jack (talk) 01:37, 18 June 2008 (UTC)
thread_title:  Comparative analysis 

message: In the types and uses section of the article, it would be good to mention the use of exon arrays in addition to exon junction arrays for use in alternative splicing detection. An exon array has probes that specifically target exonic regions within a genome sequence, avoiding exon-exon junctions. They can be used to help discover novel splice isoforms without needing prior knowledge about which isoforms are expressed.
At present, only Affymetrix manufactures and sells exon arrays, such as the Human Exon 1.0 ST Array that targets all putatively transcribed exons within the human genome. Since I work for Affy, I have a conflict of interest in editing this article to add such a note, but I'd appreciate if someone could do this. 
I also want to point out that "GeneChip" is a registered trademark of Affymetrix, as noted here: http://www.affymetrix.com/site/terms.affx. So it would be good if someone could note this as well. Thanks.  SteveChervitzTrutane (talk) 08:28, 10 September 2008 (UTC)
thread_title: Affymetrix Exon arrays and "GeneChip&reg;"

message: My edit on statistics was changed to resemble how it was before, despite being misinformative: Microarray analysis is a pain because the data is Relative  (condition A vs. B, not gene xx in A is xx pmol) and you start with an image, Analysis of SAGE data has only a fraction of the problems microarrays have, yet have lots and lots of data, so size is not #1 issue. If someone else feels so, please amend. --Squidonius (talk) 12:48, 16 November 2009 (UTC)
replies: text: Since I was the one changing the section in question, here is my response. The previous version was quite poorly worded, inviting exactly those sorts of misconceptions that it was trying to resolve. One issue that you raise is the "relativity" of the data in microarrays, which is misleading as most data are expressed as relative values (eg. concentrations, gene expression relative to a normalization genes). Overall, what you may be referring to, but what was not properly addressed, are the challenges posed by the signal-to-noise ratio, whose magnitude in microarray analysis is affected by things like hybridization (chemical noise), scanning (electronic noise), and probably most important, biological variation. So, to overcome these distinct set of challenges, algorithms have been developed, such as background subtraction, data normalization, and biological replication coupled with statistical methods that deal with issues such as multiple testing, normalization of variances, etc. that attempt to address these issues. I'm open to meaningful delineation of these issues in a new section that looks at these from a measured perspective, but I'm opposed to lumping them all together by merely saying that there are "sheer volumes of data" and "several normalization methods in the published literature" (without referencing these)—this is not helpful, as it only restates the well-known fact that microarray analysis is difficult. My modifications were aimed at recasting somewhat meandering sentences, thus trying to focus the discussion to invite further additions.  Malljaja (talk) 15:47, 16 November 2009 (UTC)
thread_title:  Statistics 

message: Better to use the term probe than feature, because it is microarray (northern blot)-specific.  — Preceding unsigned comment added by Pain-proof (talk • contribs) 01:07, 7 January 2015 (UTC)
thread_title:  principle figure 

message: Under the Data analysis section is "...in the case of commercial platforms, the analysis may be proprietary.[citation needed] "
Here is one citation, where the company clearly states their algorithm is proprietary:   — Preceding unsigned comment added by 184.100.44.130 (talk) 00:29, 9 June 2017 (UTC)
thread_title:  "citation needed" 

message: I like to think of myself as fairly scientifically literate, but after skimming through this page, and a couple of other web descriptions, I still don't understand what DNA chips are.
The most fundamental issue to explain seems missing: is this an actual biological sample taken from a living being (human or whatever) that's somehow affixed to a solid surface, or is this a purely synthetic pattern affixed to a microscope slide or other support? If the latter, why not just encode it into a computer program, why bother with a physical form at all?
I think that the people who've written about this (here on Wikipedia and elsewhere) know too much about the subject, and don't know how to introduce it to an audience who know nothing about it. I think the page should start with a much more basic explanation of what's being discussed.  — Preceding unsigned comment added by 74.104.100.218 (talk) 20:53, 30 August 2019 (UTC)
replies: text: I replaced the header figure. It was very specific on a sub-aspect on where probes of gene expression microarrays bind. Instead there now is an overview video. I hope that helps. I didn't delete the previous figure though, merely moved it down a bit LasseFolkersen (talk) 10:42, 14 May 2020 (UTC)
replies: text:  Very nice video! Very illustrative. Cool that you have made a Chinese version, but your pronounciation sucks. Good thing you put in subtitles. May I ask if you are Lasse Folkersen of impute.me? I am a big fan of that site. Why is there no wikipedia article for that? Yinwang888 (talk) 08:56, 27 May 2020 (UTC)
thread_title:  Huh?