Release Note. Agilent Genomic Workbench Standard Edition

Transcription

1 Release te Agilent Genomic Workbench Standard Edition A. New for the Agilent Genomic Workbench DNA Analytics becomes a component of Agilent Genomic Workbench DNA Analytics becomes a component of the Agilent Genomic Workbench framework, which contains new functionality, and new components. Workflow Manager Utility Desktop utility that provides a one-click solution for data analysis enabling scanned images to be turned into analyzed data through one interface. This tool is currently integrated with FE, and DNA Analytics. Sample Manager Utility Desktop utility that enables users to easily associate meta data (patient/sample information) with individual slides. The meta data is then persisted through the analysis process, making it easier to track information. Methylation Analysis The Z score calculated from the algorithm is displayed in a separate pane than log ratio. User can also calculate moving averages on these Z scores. Genome Track Operators Use AND, OR and NOT statements to combine multiple tracks to use as a sophisticated analysis filter. Differential Aberration Investigate differences in aberration profiles between two different experiment groups. UCSC Genome Browser Support View your analysis calls and genome tracks easily within the UCSC genome browser. Cluster Analysis Cluster multiple samples in to groups based upon their aberration profiles. View processed signal intensities View processed probe signal intensities across the genomic view, helping to provide copy number assignment context for the observed aberration calls. In addition each module has an extra signal pane. For Chip it displays ratios in linear scale and for Methylation the results of the algorithm (Z score) in linear pane. For CGH it displays processed signal intensities in log2 scale HMM for CGH Hidden Markov Model (HMM) for detecting probe-based aberrations is commonly used by researchers in the CGH community. Using this algorithm will help in making comparisons with other datasets not analyzed in Analytics.

2 Improved CBS algorithm New implementation of the Circular Binary Segmentation (CBS) algorithm for detecting regions of consistent copy numbers, operates up to 10X faster than what is observed in the DNA Analytics 4.0 implementation B. Known issues with the Agilent Genomic Workbench In ChIP Module, cannot generate a proper probe report for experiments with replicate arrays Within the ChIP module of analytics, a probe report can be generated for an experiment, however the replicate arrays are not combined, instead are shown together in the report. 2. On MAC, QC reports are not getting generated through the interactive mode. On MAC, QC reports are not getting generated through the interactive mode. QC reports on MAC do get generated in the workflow mode 3. Common Aberration Defect Context Corrected common aberration and aberration filter. The algorithm for context corrected common aberration expects the candidate intervals to be consecutive. When one applies aberration filters, it is not guaranteed that the filtered intervals would be consecutive. Thus. In such cases, there is an message shown ( Invalid Intervals ) Perform context corrected common aberration without aberration filters. The report generated contains the aberration summary ( score, number of probes for the COMMON interval and p value). Further selection would have to be done on this report.

3 4. On restoring experiment having large data set, some of the columns (like gene name/feature filter) in the data table are displayed blank: If users restore any experiment created from workflow with large data set, then when restore process is complete, some of the columns in the data table might be displayed blank. Mostly gene name column is displayed blank. Switching the chromosome and switching back will display the data of all the columns in the table for all the chromosomes 5. In CH3 application context, it takes time to display the TM mapping dialog after clicking Apply Probe Methylation check box: IN CH3 application context, for calcuylating probe Methylation when you check the Apply Probe Methylation check box from the menu bar, the TM mapping dialog takes time to appear. busy cursor or progress bar is displayed till the dialog appears. The application is verifying the TM information in the design files present in the application. If there are large/many designs then the time required is more. 6. In case Inter Array Replicates are combined then settings displayed in differential aberration result dialog are a bit distorted: If inter array replicates are combined for an experiment and differential aberration analysis is performed, then experiment settings displayed show a name which is a combination of the attribute by which replicates are combined and microarray name. If this name is long, then due to lack of space, it might appear a bit distorted

4 7. In stacked view rendering, tracks are not displayed properly when you dock out the gene view: If stacked view rendering is on and some tracks are displayed in UI, while undocking the gene view, the tracks are sometimes distorted. Clicking anywhere in the gene view displays the tracks in correct format.

5 A. Additional a. The HMM algorithm uses Intensity values from both the channels and masks the values with signal count less than 50 in any channel. Therefore, some of the nested calls which have signal count less than 50 in either channels would not be called separately. They may, however, still be called as part of the parent aberration. b. In Genomic Workbench we have a heatmap implementation which plots aberrant candidate intervals (not log ratios) in clustering result dialog. This is a preliminary implementation and the color settings are not adjustable. Preloaded Data These are the datasets that are preloaded into the DNA Analytics 5.0 application: Type AMADID Genome Build # Probes (Size) CH Hg (200K) CGH 3.0 Design _hg17 CGH (Both hg17 and hg18) Hg17 Hg17 Hg (6K) Hg17 = (100K) Hg18 = (100K) CGH Hg (44K) CGH Hg (244K) CGH Hg (244K) CGH Hg (244K) Exp 3.0 Design _hg17 Hg (6K) Exp Hg (44K) Exp Mm (44K) ChIP Hg (244K) ChIP Hg (244K) FE Files files 1. US _ _S01 _CGH-v4_95_Feb07_1_1 2. US _ _S01 _CGH-v4_95_Feb07_1_2 3. US _ _S01 _CGH-v4_95_Feb07_1_1 4. US _ _S01 _CGH-v4_95_Feb07_1_ files

6 System Requirements Windows XP or Server 2003 or Vista with Pentium 4 or later or Mac OS X 10.5.x with JVM 1.6 or Redhat Linux 9 2GHz CPU or greater, dual core CPU recommended 4GB RAM minimum (need more (8 GB) when working with 244K or higher microarrays) 40GB Free Disk Space 1280x768 Display minimum Installation Part 1. Install the software (Windows XP) 1. Start the installation. - If you are installing from a CD, put the CD into the CD drive. The setup program will start automatically. - If you are installing from another location, run the installation program on the computer on which you want to install the program. 2. Read the Introduction screen and click Next. 3. Read the License Agreement, click I accept the terms of the License Agreement, then click Next. 4. In the Choose Install Folder dialog box, click Next to accept the default location for installed files, or click Choose for a different destination. 5. In the Choose Shortcut Folder dialog box, select where you want the shortcut for accessing the application to be displayed, then click Next. 6. In the Pre-Installation Summary dialog box, review the list of installation parameters, then click Install. 7. When the Install Complete screen appears, click Done.

7 Part 2. Change memory settings, if necessary If you want to maximize the speed of processing, you can change the memory setting for the heap size of several processes. The heap size is controlled by two flags, Xms<size> and Xmx<size>. JVM starts with -Xms amount of memory and can grow to a maximum of -Xmx amount of memory. The 32-bit machine JVM does not support over 1400MB. To change memory settings for running Genomic Workbench In tepad, open the file.../program Files/Agilent//Genomic Workbench Standard Edition /Genomic Workbench Standard Edition lax. 2. Find the line lax.nl.java.option.additional=-xms1024m -Xmx1400m -Dsun.java2d.noddraw=true. 3. Change the flags to your preferable memory setting. For example, if you have 2 GB RAM, change the line to read lax.nl.java.option.additional=-xms1400m -Xmx1400m -Dsun.java2d.noddraw=true. te: Make sure the letter m is present at end of size and there is no space between the number and m. To change memory settings for Workflow mode 1. In tepad, open the file.../program Files/Agilent/Genomic Workbench Standard Edition /config/config_workflow.properties. 2. Find the property, HEAP_SIZE=-Xmx1200m. 3. Change 1200 to your preferable memory setting. For example, if you have 2 GB RAM, change the property to HEAP_SIZE=-Xmx1400m. for 64 bit machines the default is set to 2GB To change memory settings for the background process for importing FE data files 1. In tepad, open the file.../program Files/Agilent/ Genomic Workbench Standard Edition /config/config_FEImport.properties. 2. Find the property, HEAP_SIZE=-Xmx512m. 3. Change 512 to your preferable memory setting as you did for Workflow mode.