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LPE specifications

Information


Unique identifier OMICS_01978
Name LPE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.54.0
Stability Stable
Requirements
stats, R(>=2.10)
Maintained Yes

Subtool


  • LOWESS

Versioning


No version available

Documentation


LPE citations

 (10)
call_split

Nam Dia long, a Vietnamese folk formula, induces apoptosis in MCF 7 cells through various mechanisms of action

2017
BMC Complement Altern Med
PMCID: 5716261
PMID: 29202775
DOI: 10.1186/s12906-017-2027-2
call_split See protocol

[…] ed using the software provided by the manufacturer (Illumina Genome Studio v2011.1 (Gene Expression Module v1.9.0)) and transformed by logarithm and normalized by quantile method. Local-pooled-error (LPE) test and fold change (fc) were used to identified significant differentially expressed genes. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. Br […]

library_books

Botulinum Neurotoxin Type A Induces TLR2 Mediated Inflammatory Responses in Macrophages

2015
PLoS One
PMCID: 4390353
PMID: 25853816
DOI: 10.1371/journal.pone.0120840

[…] vation in BoNT/A-treated macrophages was demonstrated by comparison with basal expression levels in RAW264.7 cells at 0 h. A change in gene expression was considered significant if the p value of the LPE test was less than 0.05, the fold change was at least 2.0, and an alteration in gene expression occurred in all three independent experiments. For RAW264.7 cells treated with 1 nM BoNT/A, 70 genes […]

call_split

Microarray characterization of gene expression changes in blood during acute ethanol exposure

2013
BMC Med Genomics
PMCID: 3750403
PMID: 23883607
DOI: 10.1186/1755-8794-6-26
call_split See protocol

[…] rized data was filtered for log2 (RMA expression) >6 in at least six arrays; GCRMA, summarized data were filtered for log2 (GCRMA expression) >5 in at least six arrays. The Local Pooled Error T-test, LPE, [] was used to test for significance of differential gene expression across all possible pairwise comparisons in both sets of summarized data. Probe sets with p < 0.05 after False Discovery Rate […]

library_books

caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts

2011
BMC Bioinformatics
PMCID: 3230913
PMID: 21957981
DOI: 10.1186/1471-2105-12-383

[…] sed to the more outlier-sensitive measure, the arithmetic mean), caCORRECT avoids the ghosting problem by iteratively identifying artifacts and directly omitting them from calculations altogether.The LPE and CPP adjustments [] have also been suggested as a way to correct spatial flaws on microarrays. Artifact probes are identified by LPE and CPP similarly to caCORRECT, i.e. their dklr* measure is […]

library_books

Dissection of the Complex Phenotype in Cuticular Mutants of Arabidopsis Reveals a Role of SERRATE as a Mediator

2009
PLoS Genet
PMCID: 2760142
PMID: 19876373
DOI: 10.1371/journal.pgen.1000703

[…] hod, as suggested by Breitling and co-workers . This produces a good performance, in particular for replicate numbers below ten . We recently revealed that RP outperforms Cyber-T, Local Pooled Error (LPE), two-sample Bayes T, Empirical Bayes, SAM, fold change and the ordinary t-test in terms of the validity of the DEG lists . The significance of the detection is assessed in RP by a non-parametric […]

library_books

Identification of Genes Responsive to Solar Simulated UV Radiation in Human Monocyte Derived Dendritic Cells

2009
PLoS One
PMCID: 2727914
PMID: 19707549
DOI: 10.1371/journal.pone.0006735

[…] s, data were assigned to the experimental groups: non irradiated DC vs UV-irradiated DC. Statistical analysis for each of the selected groups was carried out by the local pooled error method (package LPE from Bioconductor (http://www.bioconductor.org). P-values obtained were adjusted for multiple hypotheses testing using the step-down false-discovery rate Benjamini-Hochberg procedure implemented i […]

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