Fees for Microarray Analysis Services

Statistical Analysis:

Set up fee and first 6 slides $300

Next 6 slides $50/slide

Above 12 slides $25/slide

Services include the following:

A. Quality control: We will use statistical methods to assess the quality of individual arrays, test for presence/absence of gene

expression for all genes, and provide summary plots (e.g. boxplot) and report.

B. Data normalization and test for significantly changed genes: We will apply state-of-art techniques including methods developed in Bioconductor and R statistical packages, and use ANOVA implemented in SAS to generate significant gene list for all comparisons specified by the investigator.

C. Analysis Report: We will provide a summary report of the analysis and the data matrices of the results with annotation for all the comparisons.

D. Additional information: We will provide a detailed description of the analysis for publication. For people interested in learning and doing the analysis themselves, we will provide the source codes used in the analysis and help on using the codes.

Notes:

1. Fee is based on analysis. One analysis includes a set of slides. Slides can be re-used in separate analysis. For example, Analysis A has 6 slides and Analysis B has another 6 slides. If we combine A and B, the 12 slides will constitute another analysis and the fee will be calculated separately using the 12 slides.

2. The above fee structure is normally applied to the experiments of reasonable complexity with not more than three factors
( i.e. treatment, strain, tissue). For very complex experiments (more than three factors or many levels for a factor such as time series study with many time points), an additional fee may be added.

Data Mining:

Data mining uses the results from the statistical analysis to help to explore and interpret the data, to discover new knowledge or build models for the biological phenomena under the study. Two services are available:

1. Data mining using GeneSpring: $300 per experiment

The analyses include data visualization, partitioning of interesting gene groups, Principal Component Analysis (PCA), Clustering, and Classification.

2. Analysis incorporating Biological knowledge: $300 per experiment

We will mainly use two software packages:

Gene Set Enrichment Analysis (GSEA), which uses statistical methods to find phenotypes or biological classifications such as pathways that show major impacts by the experiment.

PathwayAssist which maps expression results to protein interaction maps derived from literature.

Notes:

1. All software (GeneSpring, PathwayAssist) can be used by our clients, but they are only available on the computers in
the Bioinformatics Unit due to the license restriction. Our services include training and support (answering questions) on usage of the software.

2. There are many other methods and tools for microarray data mining. We may suggest, change, or add more tools to the analysis depending on the experiments. We also welcome suggestions from our clients.

3. We can provide limited training on microarray data mining. We encourage people to attend our Microarray Analysis Workshops.

Microarray Database

No fee structure yet. The services may include:

Data management: search, query, download, and sharing data

Data publishing: both analyzed and raw data after publication release

Data submission to public repository

General Notes:

1. All fees include the meetings with clients. The initial meeting is FREE. We encourage people to consult with us before they start the experiment. We can provide suggestions on experiment design.

2. In addition to the fee, for some projects, depending on the involvement, we may pursue co-authorship, especially for the data mining services.

Prices current as of Nov. 2005, subject to change without notice