http://www.progenygenetics.com/community/ Progeny Community » Forum: Progeny Lab - Recent Posts en Sat, 31 Jul 2010 03:46:58 +0000 http://www.progenygenetics.com/community/topic/74#post-159 Tue, 20 Jul 2010 11:57:40 +0000 ldowns 159@http://www.progenygenetics.com/community/ <p>I have a marker set of over 180 000 SNPs, but am struggling to get hold of the standard alleles for the set. </p> <p>I am under the impression (from the user manual) that the standard alleles are optional, and therefore not required, but when I try to import the genotyping data it all gets rejected with the message "Invalid SNP (no allele match for ACTG)".<br /> I am certain it has to do with the standard alleles, because I have worked them out from the genotyping data for a couple of markers, and when the markers have standard alleles defined, the genotype imports work perfectly.</p> <p>Please can someone help me with this?</p> <p>Thank you </p> http://www.progenygenetics.com/community/topic/62#post-125 Thu, 05 Nov 2009 12:19:43 +0000 Lianne Mink 125@http://www.progenygenetics.com/community/ <p>The markers are being added to the set but you may not be finding them with the search feature. The search feature will search by Alias name in a set but Marker name in 'All Markers'. So, if you have a different name stored as the alias from the marker name you will not be able to find it. Please search by the alias name after you added the marker to the set. The search should find that it was added appropriately to the set. </p> http://www.progenygenetics.com/community/topic/62#post-124 Tue, 03 Nov 2009 16:12:21 +0000 Lianne Mink 124@http://www.progenygenetics.com/community/ <p>Thanks Jamie! I'll contact you directly to sort through this issue. </p> http://www.progenygenetics.com/community/topic/62#post-123 Tue, 03 Nov 2009 11:33:18 +0000 jamie-lheureux 123@http://www.progenygenetics.com/community/ <p>We only have 2 sets in this database. We were trying to add the marker 0PVRL1-15_sn15-rs1022080 to one set and CSI_CYP1B1_rs1056836 to the other set. Thanks! </p> http://www.progenygenetics.com/community/topic/62#post-122 Tue, 03 Nov 2009 09:21:16 +0000 Lianne Mink 122@http://www.progenygenetics.com/community/ <p>How many sets do you have? What is the marker name that you are trying to add? If you would prefer to send this to send me the additional information via email, that would be fine. </p> http://www.progenygenetics.com/community/topic/62#post-121 Mon, 02 Nov 2009 18:20:37 +0000 jamie-lheureux 121@http://www.progenygenetics.com/community/ <p>We have a few markers that are in all markers that we can't get to add to sets. I have tried adding it to the set by right clicking on the set and selecting 'add markers to this set'. It seems like it gets added (and the others that were with it are added) but when we try to import into the set or search the set it can't be found. Are there any restrictions on marker names or perhaps the alias for markers in marker sets? The names seem particularly long, so I am wondering if there is a restriction on the number of characters? Thanks! </p> http://www.progenygenetics.com/community/topic/40#post-81 Thu, 23 Apr 2009 05:10:40 +0000 Rainer 81@http://www.progenygenetics.com/community/ <p>We are mostly working on plates, not on individual samples. If I had an option to filter for sample fields in ANALYSIS then I could select the individuals I want (such as make a query for "Container".<br /> In general, the PLATE option should have similar general functionalities than other containers. </p> http://www.progenygenetics.com/community/topic/40#post-67 Mon, 09 Feb 2009 10:04:52 +0000 jamie-lheureux 67@http://www.progenygenetics.com/community/ <p>I have gotten many requests from our lab for this feature. We have ended up importing a label into another field to be able to find who is actually on the plate. That means we have to update it every time we change a plate map. This would be a very helpful change. </p> http://www.progenygenetics.com/community/topic/40#post-66 Fri, 06 Feb 2009 13:03:19 +0000 Lianne Mink 66@http://www.progenygenetics.com/community/ <p>Thanks for your feedback Ginny! Are there other community members that would find this feature useful? If so, please post a reply. </p> http://www.progenygenetics.com/community/topic/40#post-65 Fri, 06 Feb 2009 12:51:00 +0000 Ginny Hughes 65@http://www.progenygenetics.com/community/ <p>Within the analysis module, it would be helpful to have an option to include only people on a particular plate in the analysis. Currently when you pull a plate into the "pedigree" box, it is not just the people on the plate that are included in the query, but everyone in the pedigree. Currently there is no way of selecting just the people on the plate for analysis. </p> http://www.progenygenetics.com/community/topic/34#post-62 Thu, 29 Jan 2009 13:03:51 +0000 khope 62@http://www.progenygenetics.com/community/ <p>I agree with the necessity of this feature as well. I've found using the G:P feature helps in addition to some fields I created. </p> http://www.progenygenetics.com/community/topic/34#post-52 Thu, 15 Jan 2009 15:39:24 +0000 jamie-lheureux 52@http://www.progenygenetics.com/community/ <p>We would also love this feature. We have not utilized pedigree level fields as much as we could because of this limited usability. We end up marking the proband with some feature and then using summary fields to capture everyone in the family. Having the ability to search by pedigree level fields in analysis would help to take that one extra step out. </p> http://www.progenygenetics.com/community/topic/34#post-51 Thu, 15 Jan 2009 14:52:26 +0000 Lianne Mink 51@http://www.progenygenetics.com/community/ <p>Thanks for your post! Currently there is not a way to query the pedigrees over pedigree level data fields in the analysis module. We are hoping to add the functionality in a future release. Are there any other community members that would like to add this functionality? If so, please post a response. </p> http://www.progenygenetics.com/community/topic/34#post-50 Thu, 15 Jan 2009 14:19:03 +0000 Ginny Hughes 50@http://www.progenygenetics.com/community/ <p>It would be most helpful to be able to query on pedigree fields (i.e we might want to pull out only pedigrees that have a familial mode of inheritance). IS there a way to do this? </p> http://www.progenygenetics.com/community/topic/30#post-46 Thu, 11 Dec 2008 11:02:44 +0000 Lianne Mink 46@http://www.progenygenetics.com/community/ <p>Lizr,</p> <p>We are aware of this issue with discrepancies. This will be remedied in the 7.5.05 release which is due out early next week. Thank you for your post! </p> http://www.progenygenetics.com/community/topic/30#post-45 Thu, 11 Dec 2008 10:32:28 +0000 Lizr 45@http://www.progenygenetics.com/community/ <p>I find the discrepency checks very useful for checking our data generated on the genome wide platform with our taqman genertaed data for validating SNP's. It is very useful to see if we have a platform issue when validating these SNP's. However Currently the database registers AB and BA as discrepent - which they aren't. This is really frustrating when you have to go through 1000's of these. I really only want to know if an genotype goes from for example AB to BB or AA, or if there is typing but the second assay is null. Currently we are working on 7.5.0.</p> <p>Can you let me know if the latest version does correct this problem? </p>