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Identification and normalization of plate effects in cDNA Microarray data

Bengtsson, Henrik LU (2002) In Preprints in Mathematical Sciences1999-01-01+01:00
Abstract
Introducing a new way of visualizing cDNA microarray data we have identified a new type of systematic variation, which we refer to as plate effects. We believe that plate effects are due to non-biological differences in the cDNA clones products spotted onto the microarray slides. By comparing the consistency of all replicates (both within and between slides) after performing 42 different normalization strategies we claim that the plate effects arenon-negligible and should be corrected for in addition to the already known intensity dependent effects. For comparison between normalization strategies we introduce a novel robust genewise variability measure, which we call measure of reproducibility. In our case, we also found that not doing... (More)
Introducing a new way of visualizing cDNA microarray data we have identified a new type of systematic variation, which we refer to as plate effects. We believe that plate effects are due to non-biological differences in the cDNA clones products spotted onto the microarray slides. By comparing the consistency of all replicates (both within and between slides) after performing 42 different normalization strategies we claim that the plate effects arenon-negligible and should be corrected for in addition to the already known intensity dependent effects. For comparison between normalization strategies we introduce a novel robust genewise variability measure, which we call measure of reproducibility. In our case, we also found that not doing background correction improves the reproducibility significantly. (Less)
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author
organization
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type
Contribution to journal
publication status
unpublished
subject
in
Preprints in Mathematical Sciences1999-01-01+01:00
issue
2002:28
publisher
Lund University
ISSN
1403-9338
language
English
LU publication?
yes
id
f7e8b3f5-5c6e-4501-ad95-343b82ad8f23 (old id 830048)
date added to LUP
2008-01-07 12:36:24
date last changed
2016-04-16 06:42:27
@article{f7e8b3f5-5c6e-4501-ad95-343b82ad8f23,
  abstract     = {Introducing a new way of visualizing cDNA microarray data we have identified a new type of systematic variation, which we refer to as plate effects. We believe that plate effects are due to non-biological differences in the cDNA clones products spotted onto the microarray slides. By comparing the consistency of all replicates (both within and between slides) after performing 42 different normalization strategies we claim that the plate effects arenon-negligible and should be corrected for in addition to the already known intensity dependent effects. For comparison between normalization strategies we introduce a novel robust genewise variability measure, which we call measure of reproducibility. In our case, we also found that not doing background correction improves the reproducibility significantly.},
  author       = {Bengtsson, Henrik},
  issn         = {1403-9338},
  language     = {eng},
  number       = {2002:28},
  publisher    = {Lund University},
  series       = {Preprints in Mathematical Sciences1999-01-01+01:00},
  title        = {Identification and normalization of plate effects in cDNA Microarray data},
  year         = {2002},
}