NDLI: Effects of spot and background defects on quantitative data from spotted microarrays

Content Provider	IEEE Xplore Digital Library
Author	Lalush, D.S.
Copyright Year	2003
Description	Author affiliation: Bioinf. Res. Center, North Carolina State Univ., Raleigh, NC, USA (Lalush, D.S.)
Abstract	We apply simulations generating realistic spotted microarray image data to study the effects of broken spots and background defects on the numerical values obtained from such images. Our simulation uses gene, spot morphology, and background properties derived from a published microarray study to generate replicates of images. We generate simulated datasets for several cases with high and low severity of spot breaks and high and low severity of background defects. One hundred replicate images were generated for each case. Each spot on each replicate image was quantified for "gene expression," using a spot-finding technique similar to those found in commercial software. Over the 100 replicates, we computed statistics for each gene. We found that spot defects had little common effect on the numerical values, except to slightly reduce the values for high-expressing genes. Background defects had significant effects all around, including increasing mean values in low-expressing genes, increasing variance in low- and high-expressing genes, and altering the skewness of the distribution of numerical values, frequently changing negatively-skewed distributions to positively-skewed. We conclude that background defects are likely to have the greatest effect on the accuracy of microarray data and should be avoided through experimental protocols enforcing careful handling of slides.
Sponsorship	Whitaker Found
Starting Page	3563
Ending Page	3566
File Size	305516
Page Count	4
File Format	PDF
ISBN	0780377893
ISSN	1094687X
DOI	10.1109/IEMBS.2003.1280922
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2003-09-17
Publisher Place	Mexico
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Bioinformatics Image generation Protocols Genomics Data analysis Analytical models Printing Morphology Statistics Gene expression
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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