http://www.progenygenetics.com/community/ Progeny Community » Forum: General Discussion - Recent Topics en Sun, 05 Feb 2012 17:52:52 +0000 http://www.progenygenetics.com/community/topic/182#post-589 Wed, 16 Nov 2011 12:36:26 +0000 Toby McHenry 589@http://www.progenygenetics.com/community/ <p>I am having some trouble viewing my Mendelian Error report for large numbers of errors. I have a genotype import with 38,000 MEs, and Progeny's behavior is inconsistent. Sometimes the report doesn't show up at all. Sometimes the report shows up with only a subset of the errors, but not the complete list. And the list cuts out at differing points on subsequent attempts.</p> <p>I would like to be able to export my full list of MEs, but this is proving difficult. Do you expect this to be so flaky for a report of this size? </p> http://www.progenygenetics.com/community/topic/232#post-668 Tue, 24 Jan 2012 16:03:42 +0000 gregm 668@http://www.progenygenetics.com/community/ <p>Hi, </p> <p>How can I determine which version of Progeny (clinical vs lab) we have installed? The "about" menu option just says it is Progeny 7.6.04. There was some talk here we might have clinical+ or something (if there is such a thing). The information was requested by a collaborator's database manger. </p> <p>thanks </p> http://www.progenygenetics.com/community/topic/231#post-664 Thu, 12 Jan 2012 17:37:40 +0000 Benjamin Fey 664@http://www.progenygenetics.com/community/ <p>When I add one of my computed fields to a spreadsheet format and subsequently run that spreadsheet, I am getting a database error and the sheet stops populating after about 100 entries. I know that there should be &gt;3000 entries. The computed field is very simple and shouldn't be overly-taxing to calculate:</p> <p>YEARDIF({Patient Demographics\Date of Birth},{Patient Demographics\Date of Diagnosis})</p> <p>where "Date of Diagnosis" is calculated by another simple formula:</p> <p>YMD( {Patient Demographics\Year of Diagnosis}, 06, 01 )</p> <p>The fields are correctly calculated when I view them as a part of the Individual Datasheets. Is there a conflict in having the two computed fields nested like this? The error popup says "A database error prevented the data from being retrieved." </p> http://www.progenygenetics.com/community/topic/230#post-659 Fri, 06 Jan 2012 13:00:56 +0000 Toby McHenry 659@http://www.progenygenetics.com/community/ <p>I don't see any way to break a custom export into multiple output files (i.e. by chrom or per N number of markers). Is this option available for custom genotype exports?</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/181#post-588 Wed, 16 Nov 2011 12:16:43 +0000 Toby McHenry 588@http://www.progenygenetics.com/community/ <p>We have recently upgraded to Progeny 8, and things seem to be going well. We have found a bug, however, which is causing Progeny 8 to crash. This used to work for Progeny 7.</p> <p>In the Pedigree section, when I select multiple pedigrees, right click to select print pedigree, and then choose PDF as the printer, Progeny 8 crashes with the error: "Progeny 8 has encountered a problem and needs to close." This is only when selecting multiple pedigrees. A single pedigree can print to a PDF without problems.</p> <p>We often want to make PDFs of many pedigree at once, so we would appreciate this fix. </p> <p>And a related request: We would REALLY appreciate the ability to print many pedigrees to a single PDF file with many pages (as opposed to a separate PDF file for each ped which requires a separate clicking of the "OK" button for each).</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/221#post-646 Tue, 06 Dec 2011 13:27:01 +0000 Tokhir Dadaev 646@http://www.progenygenetics.com/community/ <p>I have a date field in DD/MM/YYYY format. I want to create a computed field that would show the same date in YYYY/MM/DD? 111 is a JAPAN date code for YYYY/MM/DD (<a href="http://www.comsci.us/sybase/date_fmt.html)" rel="nofollow">http://www.comsci.us/sybase/date_fmt.html)</a>, so I have created a computed field as:</p> <p><code>CONVERT(datetime, {Personal\P DOB}, 111)</code></p> <p>but it still shows the date as DD/MM/YYYY when I run a IndivSS. </p> http://www.progenygenetics.com/community/topic/222#post-647 Wed, 07 Dec 2011 07:51:59 +0000 Tokhir Dadaev 647@http://www.progenygenetics.com/community/ <p>Addition of Console option into IndivSS/PedigreeSS, where user could enter basic SQL statements.</p> <p>Computed Field Editor - Computed Field Definition window could be improved, it is very basic. It is OK if the definition is couple of lines, but once I start using multiple nested IFs/CASEWHENs or SELECT statements then it is hard to keep track of things.<br /> - make the window resizable<br /> - when Test button is clicked - autoformat. example - <a href="http://www.dpriver.com/pp/sqlformat.htm" rel="nofollow">http://www.dpriver.com/pp/sqlformat.htm</a></p> <p>Bugs on Computed Field Editor?<br /> - When creating computed field in Individual level, Data Folders does not show Pedigree summary fields<br /> - When I am e.g. in Query folder, then right click to create computed field. In Editor if I drag and drop a field from Personal folder, then click Add. The field is created in Personal folder not in Query folder. </p> http://www.progenygenetics.com/community/topic/193#post-608 Tue, 22 Nov 2011 10:13:00 +0000 Daoud 608@http://www.progenygenetics.com/community/ <p>I'm having an issue with image fields. I want to have a table with multiple image fields. When I make this table it seems not possible to upload the images in the rows of this table. When I try this on the web client with the same table I do get the option to upload the images in the rows, but when I upload it gives me the error that the size of the image exceeded the limit of 1024, but the image is only 64kb? Do you have any idea how I can use a table with multiple images </p> http://www.progenygenetics.com/community/topic/183#post-591 Wed, 16 Nov 2011 15:12:27 +0000 waplesr 591@http://www.progenygenetics.com/community/ <p>Progeny 7 Suite</p> <p> I'm trying to specify two levels of location information for pedigrees as Pedigree Data Fields. Here I'll use the example of 'State' and 'County', each having its own field.<br /> My goal would have each field have a drop down menu. 'States' would have a drop down menu to select from the possible entries. 'Counties' would also have a drop down menu, but the available values would be determined by the value selected in 'State.' Some State/County combinations are meaningless so I want to restrict the possible options to those that reflect reality.<br /> I've tried various combinations of table / dropdown / and lookup tables to no avail. I'm unfamiliar with how progeny would handle a situation like this, any help would be apprecaited.</p> <p>Thanks<br /> Ryan </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/81#post-176 Tue, 12 Oct 2010 09:34:50 +0000 Toby McHenry 176@http://www.progenygenetics.com/community/ <p>I'm wondering if there's a way for a pedigree field to be displayed on the pedigree drawing. I see that as a default the Pedigree Name field appears in a header for each ped drawing. Is there a way for a user-defined pedigree field to also be displayed? Perhaps in the footer or elsewhere on the picture?</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/179#post-583 Thu, 03 Nov 2011 16:20:13 +0000 Severine 583@http://www.progenygenetics.com/community/ <p>I need you help with a computed field to calculate a volume. I have a problem in my computed expression that I don't find:<br /> {Information\Lab stock Vf (µl)}/{Information\conc nanodrop (ng/µl)}*100<br /> If I replace one of the {Information\Lab stock Vf (µl)} or {Information\conc nanodrop (ng/µl)} by a number, my expression is ok?? The two fields that I used are number. Can you tell me what's wrong?</p> <p>Thank you </p> http://www.progenygenetics.com/community/topic/173#post-561 Fri, 30 Sep 2011 11:03:58 +0000 Toby McHenry 561@http://www.progenygenetics.com/community/ <p>I was wondering if it would be possible to have a color in the ped drawings for "show linkage selections" to represent that a person has no actual genotype calls (i.e. all NoCalls and/or no genotypes imported).</p> <p>We now have people with no true genotypes, but because they were at some point imported with NoCalls, they're flagged as green in the little boxes just like people who have true calls.</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/176#post-573 Mon, 17 Oct 2011 16:22:52 +0000 stephedt 573@http://www.progenygenetics.com/community/ <p>I've looked through all the user administration options, and I can't find a way to prevent end users from deleting individuals. I am trying to restrict this so only a specific class of users has the ability to delete individuals. Is there a way to do this? </p> http://www.progenygenetics.com/community/topic/174#post-564 Fri, 07 Oct 2011 11:20:31 +0000 Toby McHenry 564@http://www.progenygenetics.com/community/ <p>I am trying to write a conditional calculated field, and I am wondering if it is possible to have the code do and ELSE IF:</p> <p>IF (condition1)<br /> THEN value<br /> ELSE IF (condition2)<br /> THEN value<br /> ELSE value<br /> ENDIF</p> <p>I couldn't get this to work. It this is possible, can you send me an example with the proper syntax? Thanks!!! </p> http://www.progenygenetics.com/community/topic/162#post-511 Mon, 25 Jul 2011 10:15:07 +0000 Tokhir Dadaev 511@http://www.progenygenetics.com/community/ <p>Progeny 7.6.00</p> <p>I need to create a computed field to calculate the risk of cancer based on Individuals genotype. This field should appear on Individual Data Sheet.</p> <p>e.g.<br /> <pre><code>Individuals cancer risk = if marker1 is AB then 1.2 else 1 * if marker2 is BB then 1.5 else 1</code></pre> <p>From Marker level I cannot see Individual level fields and vice versa. Any ideas? </p> http://www.progenygenetics.com/community/topic/172#post-558 Wed, 28 Sep 2011 11:36:03 +0000 Toby McHenry 558@http://www.progenygenetics.com/community/ <p>I recently did a Progeny Analysis PLINK Export and accidentally selected "Pedigree ID" instead of "Pedigree Name". Is there somewhere I can lookup which Pedigree ID matches which Pedigree Name? Or are they just applied numerically to the peds selected by the query. I really need to know which ped is which. This was a long export (~24 hours), so I'd rather not rerun it, but maybe I have to?</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/170#post-555 Thu, 22 Sep 2011 22:43:24 +0000 freeseek 555@http://www.progenygenetics.com/community/ <p>We have a pedigree where we assigned the wrong mother of a sample. How do we remove or change the relation from the pedigree sheet? There doesn't seem to be a clear way. Or is there no way at all? </p> http://www.progenygenetics.com/community/topic/136#post-423 Thu, 28 Apr 2011 11:48:34 +0000 Toby McHenry 423@http://www.progenygenetics.com/community/ <p>I'm still using Progeny 7, but was wondering about ID reporting in the discrepancy error report. Right now the only individual ID is a field called "Name", which sometimes looks like "Pedigree ID _ UPN", but other times is a single non-unique number. Is there a way that I can force this field to be "Pedigree ID _ UPN", or, even better, a user-defined ID field? Right now I can't tell who my discrepancies refer to with this "Name" variable unless I open each pedigree individually. I want to make a report with hundreds of discrepancies and don't want to open each one. </p> http://www.progenygenetics.com/community/topic/169#post-548 Wed, 14 Sep 2011 06:58:10 +0000 Daoud 548@http://www.progenygenetics.com/community/ <p>When I export a pedigree as XML and I want it to import again it gives a parse error. When I look at the the line of the error it doesn't show anything weird. Am I the only one who is having this problem? </p> http://www.progenygenetics.com/community/topic/117#post-313 Tue, 15 Mar 2011 04:54:23 +0000 Tokhir Dadaev 313@http://www.progenygenetics.com/community/ <p>I am trying to create a computed field "CD Age" within a table field "CD". It is giving (Bad Calculation) as it is trying to do this:<br /> YEARDIF (<br /> {Personal\P DOB},<br /> {Medical\CD Date}<br /> )</p> <p>Instead it should be like this, but it won't let me enter this formula:<br /> YEARDIF (<br /> {Personal\P DOB},<br /> {Medical\CD.CD Date}<br /> )</p> <p>Is it possible to have a computed field within a table field? </p> http://www.progenygenetics.com/community/topic/166#post-534 Tue, 16 Aug 2011 12:03:16 +0000 mccanejd 534@http://www.progenygenetics.com/community/ <p>Hello,</p> <p>Recently one of our lab workers accidentally moved nearly a thousand newly imported individuals into the wrong pedigree. My first thought was to open the pedigree, select all the individuals, and select Remove Individuals from Pedigree. However, it seems that this can only be done on a single-individual basis. My next thought was to select all the individuals and choose Delete Individuals from Database, and just start over at square one by re-importing them. However, even though I have all the individuals in the Pedigree drawing sheet selected, choosing "Delete Individual(s) from Database" only deletes one individual. So, stuck with 900+ individuals in the wrong pedigree my last resort was to delete the pedigree itself, thus deleting the individuals, and re-build the pedigree followed by re-importing the individuals. I suppose my question out of all this is, are there any plans to make removing individuals from a pedigree an easier process? I.e. being able select a list of individuals while in the individuals tab, right clicking and having a "Remove Individual(s) from Pedigree(s)" option? Or even adding the capability, while in the pedigree view, to remove multiple individuals from the pedigree rather than just one at a time?</p> <p>Thanks,</p> <p>-Jesse </p> http://www.progenygenetics.com/community/topic/140#post-434 Mon, 09 May 2011 13:51:57 +0000 Roger 434@http://www.progenygenetics.com/community/ <p>I notice that the release notes for version 7.6.07 include "Added the Merge Pedigrees feature. "</p> <p>Is there documentation available for this feature?</p> <p>Say I have two pedigrees in which several individuals are represented in both families.<br /> What is the fastest way to merge the two pedigree structures and all the associated data?</p> <p>Roger </p> http://www.progenygenetics.com/community/topic/158#post-501 Mon, 18 Jul 2011 02:30:50 +0000 swfouchier 501@http://www.progenygenetics.com/community/ <p>Is it possible when you print a plate lay-out that the plate name is mentioned on the print as well?<br /> Best, Sigrid </p> http://www.progenygenetics.com/community/topic/149#post-487 Wed, 06 Jul 2011 11:16:20 +0000 Toby McHenry 487@http://www.progenygenetics.com/community/ <p>One feature I like about Progeny's genotype import is that it keeps a record of the Mendelian Errors. Even after the error has been corrected and the check rerun, it's nice for there to be the log that an error was fixed.</p> <p>I have a question about using the tools:<br /> * Clear the genotype call for all selected rows<br /> * Clear the genotype data for the entire pedigree and marker for all selected rows</p> <p>If I pick either of these, then the log of my ME disappears from the ME list. Is this intentional? I assumed if Progeny cleared genotypes, then the record of the ME would remain, the A1 and A2 calls would go blank, and if I reran the ME checks on those rows, then they'd be grayed out as corrected. I don't want to use either clearing tool if it's going to remove my log of the ME. </p> http://www.progenygenetics.com/community/topic/163#post-522 Wed, 03 Aug 2011 10:36:04 +0000 Toby McHenry 522@http://www.progenygenetics.com/community/ <p>Hello,</p> <p>I was wondering if it is possible to create a new marker set that is a subset of existing markers in Progeny. For example, say I have several hundred thousand SNPs in Progeny, and I have a list of 500 SNPs that I want to make as a separate marker set. What is the easiest way to do that? If I try to just custom import the new list, then Progeny wants me to give chrom number and bp positions. Without exporting all the markers, grepping for my 500, and re-importing, is there an easier way to get a subset of markers from just a list?</p> <p>Thanks! </p> http://www.progenygenetics.com/community/topic/165#post-528 Thu, 04 Aug 2011 13:01:03 +0000 Conrad Brammer 528@http://www.progenygenetics.com/community/ <p>Have you ever used an RSS feed before? Have you ever wondered how it works?</p> <p>RSS is the acronym for Really Simple Syndication and it's a way that readers of a blog, or even for a form such as this, can access the contents of a blog without having to browse to a website in order to read it. The way you can do this is by subscribing to something called an RSS feed. </p> <p>What is an RSS feed?</p> <p>An RSS feed is basically a computer-readable summary of the content of a web page/blog. Progeny provides an RSS feeds for both our forum and our blog. You can subscribe to any of these feeds and have them show up right in your mailbox in a designated folder. The feeds can be general (such as all recent posts on the forum) or specific to a category such as "Software Updates".</p> <p>How do I subscribe to an RSS feed?</p> <p>There are a number of ways to add an RSS feed, but one of the easiest ways is to look for the RSS feed link on each of the sites. If there is a feed available you will see the orange RSS feed icon. Click on the icon and you will have options for where you would like to view your feed, i.e. in Outlook. To learn more about RSS feeds in Outlook 2010, take a look at their Getting Started page:</p> <p><a href="http://office.microsoft.com/en-us/outlook-help/subscribe-to-an-rss-feed-HA010355679.aspx" rel="nofollow">http://office.microsoft.com/en-us/outlook-help/subscribe-to-an-rss-feed-HA010355679.aspx</a> </p> http://www.progenygenetics.com/community/topic/160#post-505 Tue, 19 Jul 2011 18:00:57 +0000 swfouchier 505@http://www.progenygenetics.com/community/ <p>I want to export PEDs in XML export in which I adress which fields should be exported. According to the manual this is possible, but in P7 it only asks for location to export to and then it starts exporting. No field choice option anymore?<br /> Best, Sigrid </p> http://www.progenygenetics.com/community/topic/133#post-408 Wed, 20 Apr 2011 17:46:17 +0000 Benjamin Fey 408@http://www.progenygenetics.com/community/ <p>Is there a way to display the actual allele SNP values (G, C, A, T) on the haplotype of a pedigree? Several researchers in our lab have requested this, and since I did not see an option for it in the properties dialog box, I've simply been displaying them with added text. Is there built-in functionality for this? </p> http://www.progenygenetics.com/community/topic/145#post-458 Sat, 28 May 2011 05:18:49 +0000 swfouchier 458@http://www.progenygenetics.com/community/ <p>In P7 the subpedigrees are in red, why is this nog the case anymore in P8.<br /> Since not all changes made in a sub-pedigree result in the same changes in the original pedigree, like deleting individuals, I think it should be more clear that you working in a sub-pedigree. In P8 this is much less clear now with having the same colour and only a dashed line.<br /> How can I get my red subpedigrees in P8 back?<br /> Thanks,<br /> Sigrid </p>