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:8/28/2014)... A new research platform uses a ... tiny structures undergoing stress and heating, an ... designs for microelectronics and batteries., This new ... about how heating and the surface stress ... Researchers have discussed the merits of surface-stress ...
(Date:8/28/2014)... The ability for organizations to attract ... allow individuals to perform at the highest of levels, ... looking to compete in this post–recession era. The ... as the sector increasingly focuses on the importance of ... have real results on the organization's development and the ...
(Date:8/28/2014)... 2014 Sterlitech is proud to announce ... its stable of products . These additional ... and include membrane filters with surface charges. ... demand for our membrane process testing equipment, and correspondingly, ... sheet membranes,” explains Sterlitech President Mark Spatz. “The ...
(Date:8/28/2014)... Scientists, researchers, and technologists will converge ... Damage 2014 symposium. Marking its 46th year, the ... run 14-17 September. The event is sponsored by ... , The premier conference for basic and applied issues ... materials will engage researchers and engineers from numerous industries ...
Breaking Biology Technology:New analytical technology reveals 'nanomechanical' surface traits 2New analytical technology reveals 'nanomechanical' surface traits 3Klein Hersh International Leads Philadelphia Area Life Science Industry in Company Culture 2Klein Hersh International Leads Philadelphia Area Life Science Industry in Company Culture 3Sterlitech Corporation Enhances Its Selection of Flat Sheet Membrane Filters 2Laser Damage to Draw Researchers, Engineers, Scientists to 46th Annual Conference 2Laser Damage to Draw Researchers, Engineers, Scientists to 46th Annual Conference 3
... 7 Nektar,Therapeutics (Nasdaq: NKTR ) President and ... upcoming Natixis Bleichroeder Second Annual Hidden Gems,Conference in New ... at 2:30 p.m. ET., The presentation will be ... Relations, Events Calendar section of the Nektar website:, http://www.nektar.com ...
... Customer the Broad Institute of MIT and Harvard, Among ... ... 7 Isilon(R) Systems (Nasdaq:,ISLN), the leader in clustered storage, ... the growing data storage,challenges facing life science research organizations as ...
... Oct. 6 NEXCORE Technology, Inc., a,world-class original ... agreement with GI Supply of Camp Hill, Pa, ... Polar Wand is a portable,device that uses endoscopic ... gastrointestinal tract in patients resistant to conventional,endoscopic therapy., ...
Cached Biology Technology:Isilon CTO Addresses Life Science Data Storage Challenges at Harvard Medical School's BioMedical HPC Leadership Summit 2Isilon CTO Addresses Life Science Data Storage Challenges at Harvard Medical School's BioMedical HPC Leadership Summit 3NEXCORE Technology Selected to Manufacture New Endoscopic Cryotherapy Device 2
(Date:9/1/2014)... BOSTON (September 1, 2014, 10:20 AM EDT) It ... healthy low-calorie foods over unhealthy higher-calorie foods, according to ... Human Nutrition Research Center on Aging (USDA HNRCA) at ... today in the journal Nutrition & Diabetes , ... suggests that it is possible to reverse the addictive ...
(Date:9/1/2014)... animals, bats are perfectly adapted to a life without light. ... reflected echoes to measure distance to obstacles or prey. In ... delays. A study carried out by researchers at Technische Universitt ... map dynamically adapts to external factors. , Closer ... in too close to an object, the number of activated ...
(Date:8/31/2014)... blood test provides a fast and accurate tool ... study shows. The newly developed test (TAM-TB assay) ... active tuberculosis in children. The test features excellent ... combination with speed of a blood test. The ... diagnosis of tuberculosis in children, particularly in tuberculosis-endemic ...
Breaking Biology News(10 mins):Training your brain to prefer healthy foods 2Zooming in for a safe flight 2New tuberculosis blood test in children is reliable and highly specific 2
... , , , , ... , AUDIO: Learn ... , Click here for more information. ... , , , , , ...
... have begun to categorize breast cancers into four main ... cells. Which category a cancer falls into generally determines ... cancers in one of the four groups called ... particularly tricky to treat because they usually don,t respond ...
... host the U.S. book release of Women Scientists in ... of Academies of Science (IANAS). This compilation of ... to inspire students, especially young women, to pursue science ... Spanish, the book includes the stories of eminent female ...
Cached Biology News:Bad decisions arise from faulty information, not faulty brain circuits 2Bad decisions arise from faulty information, not faulty brain circuits 3Bad decisions arise from faulty information, not faulty brain circuits 4UCLA researchers find nanodiamonds could improve effectiveness of breast cancer treatment 2UCLA researchers find nanodiamonds could improve effectiveness of breast cancer treatment 3
... PCR Enhancer (with betaine) substantially improves ... and specificity for amplification of many ... in PCR eliminates the base-pair composition ... thermal stability, suppresses pauses of DNA ...
... Biotin Streptavidin-AP Systems provide rapid, precise ... antigens in frozen or paraffin-embedded tissue, ... systems also facilitate double or triple ... performed simultaneously with primary antibodies of ...
... computer controlled pre-amplifier suitable for a broad ... input for recording physiological signal such as ... transducer input for use with a wide ... options include a stimulus artefact clamp to ...
... Two sizes available for use with 96- or ... Thermo-Mat™ 96 for ease of location on 96-tube plates ... in the skirt of the plate* Efficient sealing ... used in conjunction with screw or clip-down hot lid ...
Biology Products: