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LoessM specifications

Information


Unique identifier OMICS_27400
Name LoessM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for LoessM

LoessM citations

 (4)
library_books

Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF α or IGF1

2015
PLoS One
PMCID: 4536022
PMID: 26270642
DOI: 10.1371/journal.pone.0135284

[…] Agilent Technologies). If a miRNA passed the filtering criterion “is well above background” in at least two of the replicates within one group it was retained. MiRNA microarray data was normalized by loessM normalization [,]. The Agilent microarray data was MIAME [] compliant. The miRNA microarray expression data were deposited in the ArrayExpress database [] and are accessible with the ArrayExpre […]

library_books

Impact of normalization methods on high throughput screening data with high hit rates and drug testing with dose–response data

2015
Bioinformatics
PMCID: 4653387
PMID: 26254433
DOI: 10.1093/bioinformatics/btv455

[…] importance of having controls on each plate. Another approach would be to adapt methods developed for normalizing microarray experiments such as generalized procrustes analysis () and modified Loess [loessM ()]. Generalized procrustes analysis requires replicate experiments, whereas loessM requires an experimental design based on biological replicates dye-swap. Because of the limited amount of cel […]

library_books

TNF α and IGF1 modify the microRNA signature in skeletal muscle cell differentiation

2015
PMCID: 4325962
PMID: 25630602
DOI: 10.1186/s12964-015-0083-0

[…] icroRNAs which passed the filtering criterion “well above background” in at least two of the replicates within one group were retained. 282 miRNAs met these detection criteria. Data was normalized by loessM normalization [,]. Agilent microarray data was MIAME [] compliant and was registered into the ArrayExpress database (www.ebi.ac.uk/arrayexpress) [], a publicly available repository consistent w […]

library_books

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study

2012
PLoS One
PMCID: 3377731
PMID: 22723911
DOI: 10.1371/journal.pone.0038946

[…] umber of differential expressions due to high sensitivity of the system and template amplification of qPCR. However, the higher overall miRNA expression standard deviation of 0.635±0.112/0.413±0.070 (loessM normalized platform specific/common dataset) compared to AGL array with an average standard deviation of 0.173±0.061/0.137±0.077 (loessM normalized platform specific/common dataset) indicated t […]

Citations

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LoessM institution(s)
Department of Statistical Sciences, University of Padova, Padova, Italy; Department of Biology, University of Padova, Padova, Italy
LoessM funding source(s)
Supported University of Padova (grants CPDR070805 and CPDA075919); Fondazione CARIPARO under the grant ‘A computational approach to the study of skeletal muscle genomic expression in health and disease’.

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