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Microarray Resource > Data Analysis
DATA
ANALYSIS
Procedure for Downloading
.tiff image files via password protected accounts
Created in conjunction with the Yale Center for Medical
Informatics the
Yale Microarray
Database (YMD) is
a server based system for downloading images to investigators'
personal computers under "Simple menu" feature.
Each researcher has been assigned a
four letter code and password to view a list of their own stored .tiff files. The
files may be downloaded locally and analyzed at any workstation set
up with QuantArray and Axon software - see below. Codes and passwords will be
distributed via e-mail after scanning. Questions should be directed
to Irina at irina.tikhonova@yale.edu, Lesa at
lesa.moemeka@yale.edu
Please follow this link to download .tiff
files:
Retrieve images at
YMD
Pro cedure for accessing DNA
Microarray Analysis Workstations
Two NT workstations in Academic Computing are
available on a first-come first-served basis in SHM IE 53 for
processing both ScanArray and Axon 4000A datasets.
The workstations are available for use 24 hrs per day, 7 days per
week. Card key access must be arranged in advance. Help with data
analysis is available by advance appointment with
Shanti Kunchaparty.
Please contact Shanti
Kunchaparty
shanti.kunchaparty@yale.edu for more information.
An NT
workstation at 300 George St., Suite 2117 is available
to microarray
users Monday - Friday, 9:00 AM to 5:00 PM.
The following
software is installed:
:
GeneSpring
Manual
available at work station - PLEASE DO NOT REMOVE
Axon Instuments:
GenePix Pro5TM: Accepts Axon 16 bit black and white .tif mages and
ScanArray .tif images.
Online manual
available here
Extended Analysis
Microarray numerical spreadsheet data may be analyzed
using a number of different softwares available at Yale or
downloadable from the web.
 Analysis tools at the
YMD
Papers of interest
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Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E.
Using the gene ontology for
microarray data mining: a comparison of methods and application to
age effects in human prefrontal cortex.
Neurochem Res. 2004 Jun;29(6):1213-22.
-
Rhodes DR, Chinnaiyan AM.
Bioinformatics strategies for translating genome-wide
expression analyses into clinically useful cancer markers.
Ann N Y Acad Sci. 2004 May;1020:32-40.
Review.
-
Zeeberg BR, Riss J, Kane DW, Bussey KJ, Uchio E, Linehan WM, Barrett
JC, Weinstein JN.
Mistaken identifiers: gene name errors can be introduced
inadvertently when using Excel in bioinformatics.
BMC Bioinformatics. 2004 Jun 23;5(1):80.
-
Bhattacharya S, Long D, Lyons-Weiler J.
Overcoming confounded controls in the
analysis of gene expression data from microarray experiments.
Appl Bioinformatics.
2003;2(4):197-208.
-
Lyons-Weiler J. Profound
normalisation challenges remain in the analysis of data from
microarray experiments.
Appl Bioinformatics.
2003;2(4):193-5.
-
Townsend JP.
Resolution of large and small differences in gene expression using
models for the Bayesian analysis of gene expression levels and
spotted DNA microarrays.
BMC Bioinformatics. 2004 May 05;5(1):54.
-
Asyali MH, Shoukri MM, Demirkaya O, Khabar KS.
Assessment of reliability of
microarray data and estimation of signal thresholds using mixture
modeling.
Nucleic Acids Res. 2004
Apr 27;32(8):2323-35.
-
Holzman T, Kolker E.
Statistical analysis of global gene expression data: some practical
considerations.
Curr Opin Biotechnol. 2004 Feb;15(1):52-7.
-
Barrera L, Benner C, Tao YC, Winzeler E, Zhou Y.
Leveraging
two-way probe-level block design for identifying differential gene
expression with high-density oligonucleotide arrays.
BMC Bioinformatics. 2004 Apr 20;5(1):42.
-
Pieler R, Sanchez-Cabo F, Hackl H, Thallinger GG, Trajanoski Z.
ArrayNorm: comprehensive
normalization and analysis of microarray data.
Bioinformatics. 2004 Aug 12;20(12):1971-3.
Epub 2004 Apr 08.
-
Meuwissen TH, Goddard ME.
Bootstrapping of gene-expression data improves and
controls the false discovery rate of differentially expressed genes.
Genet Sel Evol. 2004 Mar-Apr;36(2):191-205.
-
Rosenzweig BA, Pine PS, Domon OE, Morris SM, Chen JJ, Sistare FD.
Dye bias correction in
dual-labeled cDNA microarray gene expression measurements.
Environ Health Perspect. 2004
Mar;112(4):480-7.
-
Page GP, Edwards JW, Barnes S, Weindruch R, Allison DB.
A design and statistical
perspective on microarray gene expression studies in nutrition: the
need for playful creativity and scientific hard-mindedness.
Nutrition. 2003 Nov-Dec;19(11-12):997-1000.
Review.
-
Leung YF, Cavalieri D.
Fundamentals of cDNA microarray data analysis.
Trends Genet. 2003 Nov;19(11):649-59. Review.
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