http://www.progenygenetics.com/community/ Progeny Community » Tag: export - Recent Posts en Sun, 05 Feb 2012 17:41:28 +0000 http://www.progenygenetics.com/community/topic/189#post-604 Mon, 21 Nov 2011 18:55:08 +0000 Conrad Brammer 604@http://www.progenygenetics.com/community/ <p>Hi Toby, </p> <p>This issue has been logged with ticket ID C1529. It may take some time to debug this one in particular as testing requires that we reproduce the issue. Given that it takes 16 hours to complete, we will have to schedule this with our QA department at our next developer meeting which is scheduled for Friday Dec. 2nd. </p> <p>We will let you know as soon as this is addressed and what solutions we can provide. </p> <p>Thanks again for you post and patience as we address this matter. </p> http://www.progenygenetics.com/community/topic/189#post-601 Mon, 21 Nov 2011 10:46:06 +0000 Toby McHenry 601@http://www.progenygenetics.com/community/ <p>I noticed a problem with Progeny 7, and it's still occurring now that we've upgraded to Progeny 8. Whenever I do a large analysis export (for example, a PLINK export on a few hundred people with 600,000 SNPs), Progeny loses the log of the export. Thus, I have no record of what was exported, and cannot rerun the export without recreating it.</p> <p>Have you seen this before? I am concerned about how Progeny is scaling to large amounts of data. We plan to continue adding GWAS SNPs to Progeny. FYI, this export took about 16 hours to complete.</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/137#post-531 Tue, 09 Aug 2011 09:44:42 +0000 jennifer-rigdon 531@http://www.progenygenetics.com/community/ <p>Wonderful news! Thanks! </p> http://www.progenygenetics.com/community/topic/137#post-514 Mon, 25 Jul 2011 19:42:21 +0000 Conrad Brammer 514@http://www.progenygenetics.com/community/ <p>Hi Jennifer, </p> <p>Just wanted to let you know that your request to have custom exports zero out the founders parents (tracking ID - C1273) has been coded into the software and will be included in our next release. The next release is currently scheduled for the week of August the 8th. </p> <p>As always, a big thanks to you and the rest of the Progeny community for sharing your ideas and suggestions to make our software a more useful tool! </p> http://www.progenygenetics.com/community/topic/137#post-467 Wed, 01 Jun 2011 18:10:19 +0000 Conrad Brammer 467@http://www.progenygenetics.com/community/ <p>This is a feature that is new to Progeny 8. </p> <p>Much of this is detailed in our user manual, so we will first get you a copy of that. If you still have questions after reading the manual please let us know. </p> <p>Genotypes that are stored at the sample level can be exported as individual level fields if they are set as the 'Primary Sample' for that individual. Outside of this use, this data cannot be viewed or exported as individual fields. </p> <p>Hope this helps! </p> http://www.progenygenetics.com/community/topic/137#post-462 Wed, 01 Jun 2011 10:28:32 +0000 Toby McHenry 462@http://www.progenygenetics.com/community/ <p>Is the ability to import genotypes at the sample level versus the individual level something Progeny 7 can do, or is this something new with Progeny 8? </p> <p>I didn't know multiple genotypes could be stored for a single person, so I'm interested to learn more about this. If there is further documentation on this, could you direct me there? Are genotypes imported at the sample level viewable and/or exportable as individual fields? I would like to know more.</p> <p>Thanks!! </p> http://www.progenygenetics.com/community/topic/137#post-445 Tue, 10 May 2011 15:58:57 +0000 Conrad Brammer 445@http://www.progenygenetics.com/community/ <p>Thanks for the suggestion, Jennifer. </p> <p>I've logged your request as well, and your tracking ID for this request is C1273. </p> http://www.progenygenetics.com/community/topic/137#post-430 Wed, 04 May 2011 11:11:45 +0000 jennifer-rigdon 430@http://www.progenygenetics.com/community/ <p>For a lab feature to consider... having the custom export zero the founders parents :) just thought I would re-add my thought since you offered!<br /> Thanks! </p> http://www.progenygenetics.com/community/topic/137#post-429 Tue, 03 May 2011 17:56:16 +0000 Conrad Brammer 429@http://www.progenygenetics.com/community/ <p>Hello Jesse, </p> <p>Have you imported genotypes for those individuals at any point in time before you imported the genotypes for ethanol and blotter samples? </p> <p>The reason I ask is because any genotype values that had previously been stored at the "Individual Level" would not have been updated when you ran your last import. Since you imported into the "Sample Level" only, this would update genotype values for the samples while leaving all "Individual Level" genotypes intact.</p> <p>For example, if you ran a genotype import "GenoRun_A" into both the Sample AND Individual Levels, then Individual_1, Sample_1 and Sample_2 would all have genotypes from "GenoRun_A" </p> <p>Now, if you run a genotype import "GenoRun_B" into ONLY the Sample Level, then Sample_1 and Sample_2 would then have genotypes for "GenoRun_B" but Individual_1 would still have genotypes for "GenoRun_A".</p> <p>This situation might explain why you saw values for "Individual" that did not match either sample from your genotype import. If you want to clear all genotypes that are currently stored at the Individual Level you should clear the genotypes for your individuals and retain the genotypes for only the samples. You can do this by clicking the "Clear Genotyping" button from the toolbar and clearing the genotypes for your individuals. </p> <p>We will be spending several development cycles here in about 2 - 3 months that will be devoted entirely to improving Lab features. If there are any features like this that you would like us to improve upon, please let us know what you would like to see before then and I'll make sure your requests are logged into our system and addressed.</p> <p>Thanks, </p> <p>Conrad </p> http://www.progenygenetics.com/community/topic/137#post-428 Tue, 03 May 2011 12:43:20 +0000 mccanejd 428@http://www.progenygenetics.com/community/ <p>I think I may have figured out what my problem was. It turns out that neither the blotter paper sample nor the ethanol sample were selected as the primary sample for these individuals. Instead, when I right click on one of the individuals and go to "Choose Primary Sample", "Individual" was selected rather than the ethanol sample or the blotter sample. So I went through and selected the ethanol sample as the primary sample for each of the individuals, re-ran the export, and the genotypes now look much better. So it seems that when "Individual" was selected as the primary sample, it was exporting some strange mix of the two sample genotypes, even though no genotype was stored for these individuals on the individual level. It might be worth fixing this to where if you export individuals who have multiple genotypes at the sample level and where "Individual" is selected as the primary sample, blank data gets exported rather than the strange results I was seeing before. </p> http://www.progenygenetics.com/community/topic/137#post-427 Tue, 03 May 2011 12:28:30 +0000 mccanejd 427@http://www.progenygenetics.com/community/ <p>Hello,</p> <p>I've run into something strange when doing a custom export for individuals who have two different genotypes stored at the sample level. Here's a little background: recently we received a set of samples, in which there were two samples for each individual. The purpose of this study was to examine two different sample preservation methods - ethanol versus blotter paper. So I created the individuals in Progeny, and created two samples for each individual. I then imported the genotypes on the sample level. So at this point each individual had two samples, each with it's own imported genotype. However, when I ran an export of the individuals, the genotypes came out pretty wacky...in some cases the allele A and B were switched, in other cases one allele was a no call and the other an A/C/G/T, and for a few fish the exported allele A/B didn't match the genotypes for either of the samples from the raw import data. I was under the assumption that when you export genotype data for an individual that has multiple samples with their own genotypes, it would export the genotype for the individual's primary sample...any idea what might be going on here?</p> <p>Thanks,</p> <p>-Jesse </p> http://www.progenygenetics.com/community/topic/129#post-404 Thu, 14 Apr 2011 10:06:09 +0000 jennifer-rigdon 404@http://www.progenygenetics.com/community/ <p>Thanks, what would be really helpful! </p> http://www.progenygenetics.com/community/topic/129#post-403 Thu, 14 Apr 2011 09:29:43 +0000 Michael Brammer 403@http://www.progenygenetics.com/community/ <p>Jennifer,</p> <p>Currently, the Custom Export option does not allow you to zero out the parent id's of the founders. We'll add this to the list and see if we can release it in an forthcoming update. </p> http://www.progenygenetics.com/community/topic/129#post-386 Tue, 12 Apr 2011 10:46:51 +0000 jennifer-rigdon 386@http://www.progenygenetics.com/community/ <p>We often export genotypes from just a cropped portion of our pedigrees. When this is done using the FBAT option, the founders mother ID and father ID are zeroed (even if they exist in the pedigree). When this is done using the Custom option, the founders parents are not zeroed and their IDs are included, even if they are not a part of the cropped pedigree that is being exported. I was wondering about the possibility of the custom option zeroing the parent IDs of the founders. I was hoping that since this is possible via the FBAT option, it could be possible via the custom option? Any ideas you have regarding this would be nice. Thanks. </p> http://www.progenygenetics.com/community/topic/59#post-228 Sat, 04 Dec 2010 14:26:13 +0000 David DeRam 228@http://www.progenygenetics.com/community/ <p>Yes. Progeny8 links directly to the BRCAPRO BayesMendel web service. It calculates the lifetime probabilities for breast and ovarian cancer as well as the family member probabilities for carrier, BRCA1, BRCA2, and both.</p> <p>The probabilities are inserted both into the database and as a text annotation on the pedigree.</p> <p>This is a new feature in version 8. </p> http://www.progenygenetics.com/community/topic/59#post-225 Fri, 03 Dec 2010 17:33:00 +0000 hchipman 225@http://www.progenygenetics.com/community/ <p>I wanted to see if there was any new fronts in getting Progeny 8 and CaGene to interface. Thank you! </p> http://www.progenygenetics.com/community/topic/59#post-146 Tue, 20 Apr 2010 07:18:52 +0000 Anonymous 146@http://www.progenygenetics.com/community/ <p>Thanks for all staff for good response. i use Progeny 7 first time but its great. i ill tell to my all friends about this. Btw Nice to talk with you. I am really enjoy to join your group. But now I am busy to complete my <a href="http://www.mcitpguides.com">mcitp</a> and update me day to day in IT world. But it is my part time study I also like to do browsing, chating and meet peoples like you to make good and honest friends. Its my pleasure to send your article to all my freind and they also get knowledge after read you article. If you dont mind. i like to add you in the list of my friends. have a nice day and keep it up. My all best wishes with you..... </p> http://www.progenygenetics.com/community/topic/35#post-137 Wed, 06 Jan 2010 13:44:59 +0000 Roger 137@http://www.progenygenetics.com/community/ <p>I guess a data dictionary feature "up front" would be useful.</p> <p>However, If you already use MS Access or some other front end to link to the Progeny database, it is easy to output the st_datadictionary table to a query or report. </p> http://www.progenygenetics.com/community/topic/59#post-132 Wed, 09 Dec 2009 11:42:25 +0000 Conrad Brammer 132@http://www.progenygenetics.com/community/ <p>Direct interfacing with CancerGene is something we are hoping to implement in Progeny 8, but at this point it is unlikely that it will be in the initial release. We will be sure to highlight that feature when its release date is a bit more concrete. </p> http://www.progenygenetics.com/community/topic/59#post-130 Fri, 04 Dec 2009 11:22:56 +0000 khope 130@http://www.progenygenetics.com/community/ <p>Lianne - </p> <p>Are there any plans on having a working risk tool in version 8? </p> http://www.progenygenetics.com/community/topic/59#post-118 Mon, 24 Aug 2009 10:10:31 +0000 Manuel Teixeira 118@http://www.progenygenetics.com/community/ <p>Thanks Lianne. </p> http://www.progenygenetics.com/community/topic/59#post-117 Mon, 24 Aug 2009 08:23:09 +0000 Anonymous 117@http://www.progenygenetics.com/community/ <p>Thank you for your post Manuel! CancerGene does include the algorithm for calculating the risk calculation but it does not include a separate exe for the algorithm. The export was designed for the stand alone exe of BRCAPRO. Our users have notified us that CancerGene uses an updated algorithm in comparison to the stand alone exe. For that reason, we do not recommend exporting the data directly to the old exe. We are considering different options for interfacing/exporting the data directly to CancerGene in the future. </p> http://www.progenygenetics.com/community/topic/59#post-116 Mon, 24 Aug 2009 06:19:00 +0000 Manuel Teixeira 116@http://www.progenygenetics.com/community/ <p>Hi. I have just started to use Progeny 7 and I realize that it has an export modek to BRCAPRO. I use CancerGene 5 but I can not find the brca.exe it refers to.<br /> I would appreciate your help.<br /> Best regards,<br /> Manuel </p> http://www.progenygenetics.com/community/topic/35#post-92 Tue, 16 Jun 2009 13:08:44 +0000 andrea 92@http://www.progenygenetics.com/community/ <p>A data dictionary feature would be great. </p> http://www.progenygenetics.com/community/topic/35#post-63 Fri, 30 Jan 2009 18:01:53 +0000 Ginny Hughes 63@http://www.progenygenetics.com/community/ <p>yes, please put my vote in as well for a data dictionary </p> http://www.progenygenetics.com/community/topic/35#post-61 Thu, 29 Jan 2009 11:36:03 +0000 khope 61@http://www.progenygenetics.com/community/ <p>I agree as well. This would certainly be beneficial for collaborative epidemiology projects, keeping track of what fields you maintain, and avoiding redundant data collection. </p> http://www.progenygenetics.com/community/topic/35#post-57 Tue, 20 Jan 2009 11:00:05 +0000 TRAMDTRAN 57@http://www.progenygenetics.com/community/ <p>Yes, I agree this would be very useful as personnel responsible for maintaining the database may change and it may not always be obvious as to why certain data has been maintained and/or the purpose of some computed fields. </p> http://www.progenygenetics.com/community/topic/35#post-54 Fri, 16 Jan 2009 10:00:50 +0000 Anonymous 54@http://www.progenygenetics.com/community/ <p>Thanks for the feature request! Are there any other community members that would be interested in this? If so, we would like to get your feedback. </p> http://www.progenygenetics.com/community/topic/35#post-53 Thu, 15 Jan 2009 19:45:52 +0000 jamie-lheureux 53@http://www.progenygenetics.com/community/ <p>It would be nice to be able to export out a data dictionary. It could just be the name of all of the fields, the field type, and if possible, the options for drop down fields. If a description could be added when each field is created that explains that field, that description could also be exported in the data dictionary. Funding sources often ask for a data dictionary to see what type of data is being collected for a study. We currently track this in excel and have to remember to update it whenever we change or make new fields. </p>