Affymetrix GeneChip Targeted Gentyping Analysis Sftware Release Ntes GTGS Versin: 1.6 AGCC Versin: 1.0 GCOS Versin: 1.4 Tpics cvered AGCC Infrmatin fr GTGS Users GCOS Infrmatin fr GTGS Users Data Transfer Tl Infrmatin fr GTGS Users Installer Limitatins Launch and Cmmunicatin Limitatins User Activity Limitatins Assay Tracking Limitatins Data Analysis Limitatins User Interface Limitatins Miscellaneus Limitatins NOTE: GTGS has nly been verified t wrk n the Targeted Gentyping Pre-Amp and Pst- Amp cmputers. A c-installatin f Affymetrix GeneChip Cmmand Cnsle (AGCC) and GTGS n the same cmputer is nt supprted. AGCC Infrmatin fr GTGS Users Hw can I get GTGS t talk t Cmmand Cnsle (AGCC), r, Why is GTGS still cmmunicating with GCOS after upgrading t GTGS 1.6? : By default, the upgrade installer retains the settings used by GTGS 1.5. This includes registering sample tracking infrmatin with a GCOS wrkstatin, if the sftware was cnfigured t d this fr GTGS 1.5. GTGS 1.6 will either cmmunicate with GCOS, r with AGCC, but nt bth. If yu wish t use GTGS with AGCC, d the fllwing: Lg int the Pst-Amp Lab wrkstatin as a user with administrative privileges (like Administratr n this cmputer ). Launch Windws Explrer and navigate t the directry C:\Prgram Files\Apache Sftware Fundatin\Tmcat 6.0\webapps\gen\cnfig. Open the file GCOS.prperties with Ntepad. Set enabled = false Save and clse this file. The next time yu use GTGS 1.6, yu will be asked t select the lcatin t save sample files (.ARR) at the apprpriate time in the sample tracking wrkflw. 'Why is GTGS nt finding AGCC CEL files even after I select the crrect flder?:' GTGS expects the CEL files t have a name based n the experiment name used in GTGS. If yur CEL files dn't use these names, they wn't be read by GTGS. The default experiment naming cnventin fr GTGS has the frmat '(a)1234567-12345'. The default array naming cnventin fr AGCC is the full Affymetrix barcde. If AGCC hasn't indexed the GTGScreated.ARR files by the time the arrays are first washed r scanned, then AGCC will itself create ARR files, and eventually CEL files, based n the full array barcde. T avid this prblem, make sure that yu save the GTGS-created.ARR files in a flder managed by AGCC (a flder within an AGCC data rt flder), and that yu give AGCC sufficient time t index these new files, befre yu wash and scan yur arrays. T recver frm this prblem, yu ll need t create a custm experiment list that pints t the actual CEL file names. Frm Array Data, Exprt Experiment List, edit the Data File
Ch A-D clumns with the actual CEL file names, and Imprt Experiment List. Yu will first need t delete existing experiments with the same names in the desired GTGS prject. GCOS Infrmatin fr GTGS Users Multiple TG Pst-Amp Wrkstatins shuld nt pint t same GCOS Instrument Wrkstatin: GTGS is designed t have nly ne TG system exchange infrmatin with a given GCOS system. D nt cnfigure multiple TG systems t cmmunicate with ne GCOS system. It is pssible that when a sample is registered with GCOS by GTGS, it may verwrite the same sample written by anther instance f GTGS. Errr - CreateExperiment: Failure in SetupExperiment: Failure in GetPrbeArrayFrmDb: Unknwn Prbe Array <prbe array name> message: If an array type is undefined in GCOS, the user can still register a sample withut the assciated experiment inf. Only prjects cntaining supprted array types can be successfully registered with GCOS, i.e. a GTGS Array Definitin must be installed having the same name as the Prbe Array Type that exists in the GCOS database (als called a Library File). If yu are using a new assay panel, yu may need t install a new Array Definitin, and may need t btain a new Library File frm Affymetrix. Inapprpriate "ERROR DAT and CEL files d nt exist: <path t.cel file>" message: During an "Imprt Experiment Data" peratin, if file permissins aren't prperly set n the GCOS shared flder that cntains the.cel files, GTGS will reprt this message, when the message shuld actually be "<path> is nt accessible. Yu might nt have permissin t use this netwrk resurce." T verify that yu actually have a file permissin prblem, pen a Windws Explrer windw and enter in the address bar "\\<GCOS_Cmputer_Name>\GCLims\Data", and see whether yu can see the cntents f the flder. Talk t yur IT supprt staff if yu dn't have the prper permissins. "Failed t cnnect t database n [server]" generic GCOS message: This generic message n failure t cnnect appears regardless f why the cnnectin failed. This message can appear if yu are nt lgged int the current Windws sessin as a dmain user, the GCOS cmputer is ff r nt cnnected t the same netwrk as yur cmputer, the GCOS cmputer name has been changed after site installatin, the database server n the GCOS cmputer has been inadvertently turned ff, r yu are nt running GTGS frm a Pre-Amp r Pst-Amp Lab Wrkstatin. This may als happen if the GCOS cmputer is running Windws XP Service Pack 2, and the Windws Firewall r DCOM settings aren't prperly cnfigured. See Windws XP SP2 and Firewall Technical Nte fr GCOS with GTGS.pdf fr mre infrmatin. The failure t cnnect message may als appear if antivirus sftware is active n the GCOS cmputer. See Nrtn AntiVirus Technical Nte fr GCOS with GTGS.pdf fr mre infrmatin. GCOS refresh: If GCOS sftware is pen when GTGS registers experiments (with GCOS), the user must refresh the GCOS applicatin t view newly registered experiments. Data Transfer Tl Infrmatin fr GTGS Users Can't transfer all DAT and CEL data t a different GCOS cmputer: There is a limitatin in Data Transfer Tl 1.1.1 and earlier (versin 1.1.0 is installed by GCOS 1.4, but a newer versin is available frm www.affymetrix.cm). When yu are asked t "Select Data t transfer OUT," yu have multiple ways f selecting which data t transfer. If yu display yur data by DAT r by CEL, nt all f yur data will be transferred. Specifically, althugh the file(s) created by DTT cntain all the data, the assciated XML files nly include a reference t ne f the fur.dat and.cel files per experiment. When DTT is used t imprt the data t a new system, the unreferenced files are nt imprted. The recmmended prcedure fr using DTT t transfer GTGS data is t display yur data by Prjects, by Samples, r by Experiments, when yu are asked t "Select Data t transfer OUT."
Installer Limitatins Errr: -1618 Anther installatin is already in prgress. Cmplete that installatin befre prceeding with this install. If yu get this message, click OK and Next t get t the end f the install prcess. Then immediately re-run the installer twice. On the first re-run, the installer will uninstall existing cmpnents. On the secnd re-run, the installer will install all needed cmpnents. Wrng GCOS cmputer name listed in the installer: If GTGS is currently cnfigured t cmmunicate with a GCOS cmputer, the installer may display the wrng GCOS cmputer name. This will happen if there are multiple GCOS cmputers listed in the GCOS.prperties file. The installer displays the first entry it finds in this file, even if it is cmmented ut with a # prefix. This issue is limited t the displayed name within the installer, and desn't alter which GCOS cmputer GTGS cmmunicates with. Database Errr: -2147467259 Descriptin: Lgin failed fr user. The user is nt assciated with a trusted SQL Server cnnectin. If yu get this message, click OK and Next t get t the end f the install prcess. Then rename yur cmputer s that it has fewer than 15 characters. Finally, run the installer again. Antivirus sftware partially blcks the installer: On new GTGS 1.6 installs (fr which SQL 2005 Wrkgrup Editin Service Pack 2 is preinstalled), Nrtn Antivirus may prevent the SQL jbs frm being installed. Amng ther things, these jbs d rutine database maintenance and nightly backups. The slutin is t temprarily turn ff Nrtn Antivirus befre running the installer n new installs. This is nt an issue fr upgrade installs, as the jbs already exist. Launch and Cmmunicatin Limitatins Java Web Start Cache: In the event that GTGS des nt launch r when upgrading t a newer versin, the user shuld clear the Java cache. Perfrm the fllwing peratins: Launch Java Cntrl Panel: Select Windws Start Menu> Cntrl Panel > Java In the General tab, select View in the Temprary Internet Files sectin. In the Java Cache Viewer windw, select all applicatins and click the X icn (remve selected applicatins). Clse the Java Cntrl Panel windws. Finally, click the GeneChip Targeted Gentyping Analysis Sftware link frm the GeneChip TG Sftware hme page. A fresh cpy f GTGS will be dwnladed fr use. Clearing the cache may als reslve ther prblems. Perfrming this peratin des nt affect saved data and des nt need t be perfrmed n a regular basis. Java Web Start Security Warning Infrmatin: Upn selecting GeneChip Targeted Gentyping Analysis Sftware frm the GeneChip TG Sftware hme page, the user must press the Start buttn n the Java Web Start Security Dialg in rder t install and run the cde. This prmpt will ccur the first time each Windws user launches GTGS, and als when GTGS is either updated r cleared frm the Java cache. Fr mre infrmatin abut the Java Web Start Security Warning please visit http://java.sun.cm. NT Authenticatin Errr" n applicatin launch: GTGS will nt launch, displaying this message. This message will crrectly appear if an unauthrized user is trying t run GTGS. Hwever, this errr message may als appear if the date n the lcal cmputer is different than the dmain date, and if during installatin GTGS was cnfigured s that the users aren't asked t select their names during applicatin launch.
User Activity Limitatins Multiple users simultaneusly editing infrmatin may lead t database errrs: GTGS desn't cntinuusly synchrnize the infrmatin in applicatin memry with what's in the database. If tw r mre users are accessing the same infrmatin and ne user adds/mdifies/deletes sme infrmatin, the ther users wn't be aware f the changes. This can lead t duplicated wrk at best, and at wrst multiple database errrs. T prevent this frm ccurring, all users shuld avid changing infrmatin in the same prject frm multiple cmputers at the same time. Users shuld als clse GTGS when nt in use. If GTGS is inactive fr an extended perid, the user shuld perfrm a "refresh" peratin (accessible frm the View menu r by pressing F5) befre any additinal changes are made. The nly way t recver frm undesirable deletins f data is restre the entire database frm a previus backup, which will lse any changes made since the backup. Database restre instructins are prvided in the GTGS Sftware User Guide, Data Strage and Server Maintenance chapter. Refresh Applicatin: If GTGS is displaying utdated infrmatin (mre r less items than shuld be appearing), select Menu > View > Refresh (r press the F5 key). If refreshing (clearing applicatin memry f utdated infrmatin) desn't help, restart GTGS. Failed t get viewer errr: Generated when user #1 is saving a cluster and user #2 tries t access the cluster nt yet saved. After the cluster has been saved t the database, user #2 can access the data. T refresh the view perfrm the fllwing peratins. First select a different tab i.e., Samples then navigate back t the saved cluster. Lcal Administratr can always run GTGS: The lcal administratr f the GTGS cmputer hsting the GTGS database and applicatin server is able t use the GTGS. This is the case even if Windws NT authenticatin is used t limit user access, and the lcal administratr is nt explicitly given permissin t use the sftware. Passwrd needed fr Admin user: If the applicatin is cnfigured s that a user des nt have t select their name frm a list when the applicatin launches, then the applicatin assumes the user is the same as the user wh lgged int Windws ("NT Authenticatin"). In this situatin, when a user selects "Set Admin User" frm the Tls menu, the user is asked t enter the admin passwrd. If this is the first time that this peratin is perfrmed, the user can create an admin passwrd. This feature is nt dcumented elsewhere. Hwever, if the applicatin is cnfigured s that a user selects their name frm a list when the applicatin launches, any user can select the admin user withut needing t enter a passwrd. Nte that the GTGS admin user is independent f the Windws Administratr. Hw t reset the Admin user passwrd. If the applicatin has asked fr an admin passwrd, but yu've frgtten the passwrd, here is hw t reset the passwrd. Lg int the Pst-Amp Wrkstatin as a user with Administrative privileges. Fr GTGS 1.5 -> 1.6 upgrade systems: Navigate t Start Menu > Prgrams > Micrsft SQL Server > Enterprise Manager Expand the tree in the left pane by selecting Micrsft SQL Servers > SQL Server Grup > (lcal) (Windws NT) > Databases > Gen > Tables Right-click n the UserTable entry in the right pane, and select Open Table > Return all rws... Find the rw f the table where UserName is admin. In this rw, duble-click the encrypted Passwrd entry, and delete it. Click the Exclamatin Pint icn (Run). This will refresh the table. An empty Passwrd field verifies that yu've reset the passwrd.
Fr new GTGS 1.6 systems: Navigate t Start Menu > Prgrams > Micrsft SQL Server 2005> SQL Server Management Studi Expand the tree in the left pane by selecting [cmputer name]> Databases > Gen > Tables Right-click n the UserTable entry in the right pane, and select Open Table Find the rw f the table where UserName is admin. In this rw, duble-click the encrypted Passwrd entry, and delete it. Click the Exclamatin Pint icn (Execute SQL). This will refresh the table. An empty Passwrd field verifies that yu've reset the passwrd. Restart GTGS. Frm the GTGS Tls menu, select Set User. Select the Admin user, and then edit yur passwrd. Assay Tracking Limitatins Experiment Names are nt unique: Neither GTGS nr GCOS supprt duplicate experiment names. During the Hyb n Arrays peratin, GTGS uses the array barcde t create the experiment name. If the riginal Affymetrix barcde is scanned, the last twelve digits f the barcde becme the experiment name. Hwever, it is pssible (althugh very rare) that tw different arrays will have the same last twelve digits. If this happens, yu will get an errr. Wrk-arunds are t use a different array, t place a different barcde n the same array, r t manually create a unique experiment via GCOS and create a GTGS experiment list entry with this new experiment name. java.lang.arrayindexoutofbundsexceptin: 0 Unhandled Exceptin appears when imprting a sample plate. T reslve, brwse t the sample plate file befre pressing Imprt. Data Analysis Limitatins Maximum recmmended prject size: The larger the data set is, the mre time will be necessary t gentype the data and display certain infrmatin. It is recmmended that yu limit t 5000 the number f experiments within any single prject. If yu knw that yur prject will invlve 5000 r mre samples, yu shuld segregate yur data int multiple prjects f similar size. Prcessing appears t hang n Insert Nrm Data: When a user perfrms a "Prcess" peratin within the "Imprt Experiment Data" windw, the first experiment prcessed may take additinal time, smetimes n the rder f several minutes. Subsequent experiments will be prcessed much mre quickly. java.lang.arrayindexoutofbundsexceptin appears when trying t View Experiment Details. If this happens, clse the Experiment Details windw, select Menu > View > Refresh (F5 key), then repeat the peratin. The field [Descriptin] is limited t [255] characters. Please revise yur entry" appears when trying t save Gentype Results t the database, after having entered a descriptin with mre than 255 characters. Unfrtunately, fllwing the suggestin desn t allw fr a save. The wrkarund is t cancel the gentyping peratin, select Menu > View > Refresh (F5 key) t remve the false Gentype Result in the tree, and then repeat the peratin (using a shrter descriptin the next time). Exprt Gentypes Results peratin cntinues if cancel after a partial save: In the middle f an exprt, if yu press the Clse buttn, and click Yes t abrt the peratin, the file exprt will appear t have been cancelled. Hwever, the save peratin still prceeds in the backgrund. The nly way t stp this is t quit the applicatin.
User Interface Limitatins Pssible lng idle time during navigatin: An hurglass icn may ccasinally appear when the user navigates t a different part f GTGS, r when ding an peratin. This will happen whenever GTGS is accessing the database r prcessing lcal data. This is a nrmal ccurrence, and the mre infrmatin needed t be retrieved r prcessed, the lnger the idle time will be. Windws flder appears empty: This is always the case when selecting the Windws flder that cntains the.cel files t be read int GTGS. Hwever, if a user is using the GTGS Open/Save windws t navigate t a different flder, an errr message shuld appear if the user is brwsing t a flder that (s)he desn't have permissin t access (the errr message wuld be " <path> is nt accessible. Yu might nt have permissin t use this netwrk resurce.") Hwever, instead it appears that yu can g int the frbidden flder, but the flder appears t be empty. Custm zm settings are lst: This ccurs whenever the axis display ptin is changed n a chart viewer. Miscellaneus Limitatins Inapprpriate External Srt n sme table clumns: The external srt peratin is nt valid fr numbers cntaining decimals and will nt prperly srt. The feature was nt designed fr srting decimal frmats, but is still enabled n sme f the tables cntaining decimal values. The desired srt can always be btained by srting n anther clumn such as a primary key, integer r alpha-numeric value. java.i.filentfundexceptin appears when exprting an assay panel. T reslve, repeat this peratin withut typing a file name in the File Name field. This dialg nly requires a directry t be selected. "NullPinterExceptin": If this message ccurs, select Menu > View > Refresh (F5 key), then repeat the peratin. If refreshing desn't help, restart GTGS.