tag:blogger.com,1999:blog-8532065960756482590.post8185076191620100624..comments2024-03-20T03:17:16.259-04:00Comments on Jermdemo: When can we expect the last damn microarray paper?Jermdemohttp://www.blogger.com/profile/01662705354227625640noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-8532065960756482590.post-76081870023731390942013-10-30T10:38:51.941-04:002013-10-30T10:38:51.941-04:00Sounds interesting, but needs a more punchy title....Sounds interesting, but needs a more punchy title. How about "Lessons form the Dog Dick Transcriptome"?Anonymoushttps://www.blogger.com/profile/14715221648229631380noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-2693224056141934712013-10-30T09:56:24.404-04:002013-10-30T09:56:24.404-04:00Eric you might want to move on to "A high-thr...Eric you might want to move on to "A high-throughput sequencing study of differential expression in dog scrotal tissue"Jermdemohttps://www.blogger.com/profile/01662705354227625640noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-16791002242488820522013-10-29T14:20:01.729-04:002013-10-29T14:20:01.729-04:00Hey, that was just about my next paper: "Micr...Hey, that was just about my next paper: "MicroPiPerl: A new Perl script to assist in pipette calibration for microarray experiments"... :( Thanks, Jeremy, now my subject is burnt.Anonymoushttps://www.blogger.com/profile/14715221648229631380noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-42601131568708561892012-03-08T07:48:35.754-05:002012-03-08T07:48:35.754-05:00Thanks Jeremy, very interesting! We have recently ...Thanks Jeremy, very interesting! We have recently released InSilico DB (http://insilico.ulb.ac.be) to manage and store genomics data, There are 100,000s of public microarray samples pre-installed available for download or export in a ready-to-use format (R and GenePattern).alain colettahttps://www.blogger.com/profile/09518884923538952652noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-12821362772773751142012-01-20T08:37:28.424-05:002012-01-20T08:37:28.424-05:00Oh this was intended to be a tongue-in-cheek post....Oh this was intended to be a tongue-in-cheek post. However, I think a statistician who writes paper in 2012 about microarray normalization is grave digging. I have no problem with people using microarrays in GWAS or clinical apps, but putting "microarray" in the title is as superfluous as "pipette" or "Perl".Jermdemohttps://www.blogger.com/profile/01662705354227625640noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-21729512545638154802012-01-20T02:32:57.483-05:002012-01-20T02:32:57.483-05:00Thanks! Very useful code. Although... Im an ecolog...Thanks! Very useful code. Although... Im an ecologist and never worked with microarrays/dont know much about them. Why the beef with them vs NGS?Bernard W.T. Coetzeehttps://www.blogger.com/profile/14401669906374994035noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-85171210615262403742012-01-19T08:21:59.975-05:002012-01-19T08:21:59.975-05:00The masters programme i am doing at one of the Uni...The masters programme i am doing at one of the Universities in Sweden is almost entirely based on microarrays. Everything we have learnt in courses such as programming in R, Genomics, Bioinformatics etc is full of microarray data analysis and NGS is totally lacking! Why haven't universities like this one revised their curricula to integrate NGS given its increasing importance in identification of disease-causal variants and clinical applications (personalised medicine)? <br /><br />I am going to use NGS data in my thesis but it will be a personal effort since even the would be supervisors have no expertise in analysing NGS data! Well, i have written this in the course evaluations and i hope they will catch up in the near future.Tjb LaMachttps://www.blogger.com/profile/14861509785787660714noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-3812583067254324952012-01-19T08:12:20.366-05:002012-01-19T08:12:20.366-05:00I think the difference is that these are only pape...I think the difference is that these are only papers with 'microarray' in the titles, and are thus probably have some flavor of statistical methodology or normalization/preprocessing. I would guess that most biology papers that use microarrays as a tool do not put the word microarray in the title, and since microarrays are a cheap, high-throughput tool with an established analysis pipeline, they, as a tool, are going to be around for a long time.Andrew Jaffehttps://www.blogger.com/profile/16582830627116028007noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-7189145825877926312012-01-19T05:38:57.527-05:002012-01-19T05:38:57.527-05:00In science just like in tecnology innovation happe...In science just like in tecnology innovation happens at a fast pace but all new technologies then have a long tail before they eventually die out.<br /><br />The same is true with microarray technology. I would not be suprised if there is a resurgence in microarray studies that microarrays are used as a complement of NGS analysis.<br /><br />I believe there is still innovation in this area and 2017 is way too optimistic (or pessimistic) view... I bet there will still be coming out with papers featuring microarrays in 15 years time.Duartehttps://www.blogger.com/profile/13960784528179885911noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-26839889666037997722012-01-19T05:02:16.372-05:002012-01-19T05:02:16.372-05:00Great post! Thanks for sharing your thoughts and y...Great post! Thanks for sharing your thoughts and your code.<br /><br />I agree with Chris, indeed the content accumulated on microarray, especially gene expression is huge and probably holds answers to open problems in biomedicine. One of the most exciting applications is drug repositioning.<br /><br />Since you can identify subjects based on their NGS data, it is not clear whether there will soon, if ever, be such a large corpus of genome-wide NGS information form such varied sources, due to privacy issues.<br /><br />The isa-tab initiative is great as it will ultimately make it easy to use this vast resource. In the meantime we are developing InSilico DB, following a pragmatic approach where users can edit the meta-data online (>118,000 profiles re-annotated to date). The numerical data is re-normalized and ready to be analyzed in open-source GUI (GenePattern) and command-line tools (R/Bioconductor). We also include RNA-Seq expression estimates from SRA, but I expect the microarray data to stay relevant for a while. If you want to check it out: http://insilico.ulb.ac.be.David Y Weisshttps://www.blogger.com/profile/02321005870365890427noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-85986971128642446732012-01-19T02:47:21.188-05:002012-01-19T02:47:21.188-05:00Ha! We do!
Yes, we reallly still write about micr...Ha! We do!<br /><br />Yes, we reallly still write about microarrays now and then. And I think we have good reasons to. Technology is just a means to an end, right? People already did lots of microarray studies and for most of these the raw data are stored in online repositories. With increased standardisation in study descriptions (e.g. The isa-tab initiative), the possibilities to use these old data in comparative studies increases. In that case you want to be sure these old data are good so you need the right normaiisation and especially quality control approaches.<br /><br />Also some of microarray technologies like ChIP-on-chip and DNA mathylation arrays are still developing and approaches for these are sometimes different.<br /><br />And finally... For some things like getting the right SNP calls microaarays just perform very well. <br /><br />So 2016? No I don't think so, the last microarray paper will probably be a lot later.Chris Evelohttps://www.blogger.com/profile/17224981213656983957noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-90259346543473940912012-01-19T02:33:09.406-05:002012-01-19T02:33:09.406-05:00Funny post :)Funny post :)Marcin Piechotahttps://www.blogger.com/profile/14045995862925193174noreply@blogger.comtag:blogger.com,1999:blog-8532065960756482590.post-90965773154947620772012-01-19T01:00:06.521-05:002012-01-19T01:00:06.521-05:00Great post and code, very useful - thank you!Great post and code, very useful - thank you!Tal Galilihttps://www.blogger.com/profile/10009278769907250225noreply@blogger.com