Change search
ReferencesLink to record
Permanent link

Direct link
Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry
Lund University.
Show others and affiliations
2007 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 23, no 11, 1401-1409 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: Pre-processing of SELDI-TOF mass spectrometry data is currently performed on a largel y ad hoc basis. This makes comparison of results from independent analyses troublesome and does not provide a framework for distinguishing different sources of variation in data. Results: In this article, we consider the task of pooling a large number of single-shot spectra, a task commonly performed automatically by the instrument software. By viewing the underlying statistical problem as one of heteroscedastic linear regression, we provide a framework for introducing robust methods and for dealing with missing data resulting from a limited span of recordable intensity values provided by the instrument. Our framework provides an interpretation of currently used methods as a maximum-likelihood estimator and allows theoretical derivation of its variance. We observe that this variance depends crucially on the total number of ionic species, which can vary considerably between different pooled spectra. This variation in variance can potentially invalidate the results from naive methods of discrimination/classification and we outline appropriate data transformations. Introducing methods from robust statistics did not improve the standard errors of the pooled samples. Imputing missing values however-using the EM algorithm-had a notable effect on the result; for our data, the pooled height of peaks which were frequently truncated increased by up to 30%.

Place, publisher, year, edition, pages
2007. Vol. 23, no 11, 1401-1409 p.
National Category
Bioinformatics and Systems Biology Probability Theory and Statistics
URN: urn:nbn:se:kth:diva-61510DOI: 10.1093/bioinformatics/btm104ISI: 000247781300013PubMedID: 17387110OAI: diva2:479281
QC 20120119Available from: 2012-01-17 Created: 2012-01-17 Last updated: 2012-01-19Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Rydén, Tobias
In the same journal
Bioinformatics and Systems BiologyProbability Theory and Statistics

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 16 hits
ReferencesLink to record
Permanent link

Direct link