Navigation Links
Extended data analysis using DeCyder EDA

ser license 28-4012-03

DeCyder 2-D Differential Analysis Software v6.5, preinstalled network 28-4012-01
(including PC and single concurrent network user license)


Analysis
Original data set
The original data set was a BVA workspace from a study on human ovarian cancer. All samples were classified by pathologists into one of the following three groups: normal, benign, or malignant. A subset of samples from 18 patients (three normal, four benign, 11 malignant) was run in duplicate and used to perform all subsequent analysis. For the classifier, nine (one as duplicate) “unknown” patients were used to verify the analysis, as well as the classification made by the pathologists.

Workspace
We created our EDA workspace by importing the BVA workspace from the cancer study. No statistical values from the BVA workspace were copied into the EDA workspace. Standard spot maps from the master and matched gels (to provide matching information) were copied into the EDA workspace but were not included in the actual analysis.

Experimental design
In the BVA workspace we imported, an experimental design was already defined. This was transferred to the EDA workspace.

Base set creation
The starting material (biopsy tissue) had a large variation, from both the inherent biological variation and the sample preparation. This led to a situation where only a small number of proteins was present in all spot maps or not matched.

For our cancer study we decided to filter out unassigned spot maps (master image and other spot maps not assigned to given groups), as well as proteins present in less than 80% of the spot maps. The remaining spot maps and proteins comprised
'"/>

Source:


Page: All 1 2 3 4 5 6 7 8 9 10

Related biology technology :

1. High-throughput gene expression analysis to screen for anti-asthma drugs
2. Fully automated DNA purification and efficient multiplex PCR for analysis of microsatellite loci
3. Flow cytometric analysis of human primary cells using the Agilent 2100 bioanalyzer and on-chip staining
4. 2100 expert software Powerful software for the analysis of RNA, DNA, proteins, and cells with the Agilent 2100 bioanalyzer
5. Using the Agilent 2100 bioanalyzer for quality control of protein samples prior to MS-analysis
6. Microfluidic analysis of multiplex PCR products for the genotyping of Helicobacter pylori
7. High resolution DNA analysis with the DNA 500 and DNA 1000 LabChip kits
8. 2D-LC analysis of phosphopeptides in brain tissue using Ettan MDLC and Finnigan LTQ
9. Neurite outgrowth cell-by-cell analysis using the IN Cell Developer Toolbox
10. Laser Capture Microdissection of muscle fiber populations and expression analysis by RT-PCR
11. TSKgel ODS-100Z and TSKgel ODS-100V column series provides a universal solution for the analysis of samples containing acidic, basic, polar & non-polar compounds
Post Your Comments:
*Name:
*Comment:
*Email:
TAG: Extended data analysis using DeCyder EDA

(Date:5/17/2013)... The paradigm of ‘one drug, one ... can help predict the adverse and therapeutic effects of ... of Computational Biology at the Genomics Laboratory, Covance, will ... high-quality genomics when used as part of the QC ... data sets to identify key clinical targets even in ...
(Date:5/17/2013)... CA (PRWEB) May 17, 2013 IAC Industries ... Technologies, a start up laboratory needing to set up and ... moving to a larger facility within a year’s time. How ... knowledge that the laboratory is temporary? What is efficient and ... Series modular workstations from IAC Industries. The planners at DisperSol ...
(Date:5/16/2013)... ISPE announced today that ... the newly created position of Vice President of ... be responsible for stimulating ISPE’s revenue growth by ... Society’s Member-led and staff-driven business model, initiating integrated ... membership and product marketing. , “Barbara joins ISPE ...
(Date:5/16/2013)... Ill. (PRWEB) May 16, 2013 ... and portable models, from Cole-Parmer is designed to ... enhanced line includes: , The new Cole-Parmer® ... true workhorses in the lab. They ensure a ... and plasma specimen separation. Their standard four-place swinging ...
Breaking Biology Technology:New Downloadable Success Story: “How To Outfit a Dynamic Lab in Flux” 2ISPE Names Barbara A. Myers, CAE, as Vice President of Professional Development 2Cole-Parmer Offers Enhanced Selection of Centrifuges 2
... second can make the difference between life and death, ... sensors" that allow for faster response times from military ... NC State that will help ensure those sensors will ... Afghanistan or elsewhere. "We,ve taken a sensor material ...
... ... of 2007 and to enhance patient safety with complete part traceability, can now use ... coding, scan and software tracking of each part and batch, including all leak test, ... ...
... the pleasantness of novel odors, just like a human ... notion that smell is completely personal and culture-specific. The ... Wolfson Medical Center, argue that the perception of an ... and it is only within specific contexts that personal ...
Cached Biology Technology:InterTech Development Company UDI System Announced 2Odor pleasantness shown to be partly hard-wired 2Odor pleasantness shown to be partly hard-wired 3
(Date:5/18/2013)... An increasing number of U.S. children are experiencing ... to research presented at Digestive Disease Week (DDW). ... at the Cleveland Clinic Children,s Hospital found that ... breath compared to their lean counterparts. The pattern ... can be correlated to potential complications associated with ...
(Date:5/17/2013)... of New Jersey, and City University of New York ... that effectively clears organisms to be viewed under ... hydrate, which is one of the few high-quality clearing ... the Drug Enforcement Administration (DEA) due to its use ... are vital for viewing organisms under a microscope. Without ...
(Date:5/17/2013)... 17, 2013, Shenzhen, China---- Why Tibetan antelope can ... Plateau? In a collaborative research published in ... and other institutes provide evidence that some genetic ... to harsh highland environments. The data in this ... genetic mechanisms and the biology of other ruminant ...
Breaking Biology News(10 mins):New research identifies risks, interventions for children's GI health 2New research identifies risks, interventions for children's GI health 3New formula invented for microscope viewing, substitutes for federally controlled drug 2New formula invented for microscope viewing, substitutes for federally controlled drug 3The genome sequence of Tibetan antelope sheds new light on high-altitude adaptation 2
... clock, from the alarms that startle us out of our ... clocks that remind us when it,s time for meals, after-school ... ubiquitous timekeepers, though, we have internal "clocks" that are part ... rhythms, regulating everything from our sleep-wake cycles to our appetites ...
... named the recipient of the 2010 Volvo Environment Prize. The ... the biology of global change, and has been widely recognized ... idea that biodiversity is a key piece in ecosystem functioning." ... November 2010. Harold Mooney is a professor of environmental ...
... NY, September 17, 2010September is National Childhood Obesity Awareness ... children and adolescents in the United States. A multidisciplinary ... weight management and should draw from the latest medical ... all of which are presented and debated in the ...
Cached Biology News:Tick tock: Rods help set internal clocks, biologist says 2
Includes USB cable, custom driver and one roll of thermal paper...
Mycoplasma and virus tested...
... 10X BlueJuice Gel Loading ... easy loading and tracking ... agarose or native polyacrylamide ... features higher density sucrose ...
Ready-to-use solution....
Biology Products: