http://www.progenygenetics.com/community/ Progeny Community » Recent Topics en Sun, 05 Feb 2012 16:52:55 +0000 http://www.progenygenetics.com/community/topic/238#post-681 Fri, 03 Feb 2012 17:43:10 +0000 freeseek 681@http://www.progenygenetics.com/community/ <p>I want to import a table we have with information about samples. Though, the samples don't exist in Progeny, so they are not going to match anything pre-existing in the database. I would like for them being created. Is this possible? Or do I have to create them first one by one and then import the data? </p> 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/220#post-644 Mon, 05 Dec 2011 16:30:14 +0000 guyygarty 644@http://www.progenygenetics.com/community/ <p>I would like to add a calculated field to a sample, that shows the time/date 44h after a reaction is executed (or after a workflow stage is executed). Is there any way to access the info in the sample Audit? If not, is there a way to route the current date and time into a static field?<br /> guy </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/214#post-637 Thu, 01 Dec 2011 23:56:05 +0000 ERamigenics 637@http://www.progenygenetics.com/community/ <p>I know that you can change the proband arrow in the properties of each pedigree, but is there a way to change it to a default UL position for every pedigree in a folder? It's very frustrating to have to change each time I add a pedigree. Thanks! </p> http://www.progenygenetics.com/community/topic/122#post-342 Tue, 05 Apr 2011 04:57:54 +0000 Daoud 342@http://www.progenygenetics.com/community/ <p>It seems that the one-click add feature in Progeny 8.1 doesn't work for pedigrees that already exist. It works fine for creating new pedigrees but not for existing pedigrees.</p> <p>Kind regards,</p> <p>Daoud </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/178#post-582 Thu, 03 Nov 2011 16:09:15 +0000 Severine 582@http://www.progenygenetics.com/community/ <p>Hi,<br /> What is the faster way to assign the next workflow stage to a multiple of aliquots? Currently, I scan the aliquot barcode, right clic to current stage to move the aliquot to the next stage and I do this for each aliquots. Is it possible to create an action for that?<br /> Thanks </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/175#post-572 Mon, 17 Oct 2011 12:36:26 +0000 mccanejd 572@http://www.progenygenetics.com/community/ <p>Hello,</p> <p>I've noticed that dragging and dropping samples onto a plate while in the plate viewer module only allows loading of samples onto the plate by row (across). In our lab protocols, we build our plates by column (i.e. sample 1 in A1, sample 2 in B1, sample 3 in C1...sample 9 in A2, sample 10 in B2, etc.). It would be very useful for us if there was an option in Progeny to toggle the loading of samples onto a plate by column or by row when using the drag and drop method. This function would save us a lot of time over importing a .txt file. Any chance we could see this feature in a future Progeny update?</p> <p>Thanks!</p> <p>-Jesse </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/139#post-432 Sat, 07 May 2011 13:20:02 +0000 Manuel Teixeira 432@http://www.progenygenetics.com/community/ <p>Hi.</p> <p>I have two issues with BRCA analysis in Progeny8.</p> <p>1- There is an issue with risk calculation using my wired web connection at work with a proxy server (it works perfectly at home and using a wireless internet connection). I contacted my Informatics department and they allowed access to the web address <a href="http://bayesmendel.dfci.harvard.edu/risk/" rel="nofollow">http://bayesmendel.dfci.harvard.edu/risk/</a> without going through the firewall, but still no success. It is not evident in the program menus how to set up a proxy in Progeny. I think that Progeny8 has a problem to access the internet via a proxy server that did not existed with Progeny7, because when I start the program not even the Progeny logo and the banner appear in the login window. This does not happen with Progeny8 when I use the laptop at home and it did not happen before with Progeny7 at work. Any help with this?</p> <p>2- I have tested the web risk calculation (using my private wireless internet access) and it works fine for calculating the mutation probability. However, the disease risk and mutation probability calculation is the same irrespective of indicating in the BRCA tab whether or not a mutation has been found in the family. This works correctly in CaGene. It seems like the information in the fields "BRCA1 test results" and "BRCA2 test results" are not taken into account in the calculation. Is this being corrected?</p> <p>Looking forward for your feedback, I send you my best regards,<br /> Manuel </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/168#post-542 Thu, 08 Sep 2011 12:49:04 +0000 kai 542@http://www.progenygenetics.com/community/ <p>Hello,<br /> I try to import data into table field using the "Global ID" as unique ID<br /> I met a problem when I try to import the data.<br /> after I click import button, I check “import into tables only” box, then click OK.<br /> A window “import cancelled” pop up, say “no tables were found in this spreadsheet, please check your settings.”</p> <p>Do you know how to solve the problem? May I need to setting something before I try to improt data into table field?<br /> Thanks,<br /> Kai </p> http://www.progenygenetics.com/community/topic/167#post-539 Thu, 01 Sep 2011 16:33:24 +0000 kai 539@http://www.progenygenetics.com/community/ <p>Hello all,<br /> When I try to import some new data into progeny, I set "pedigree name" and "UPN" as unique idenitfier. But when I import the data, just a part of of data can be imported.<br /> Do you know what the problem is? and how to solve the problem?<br /> Thanks,<br /> Kai </p>