matchprobes specifications

Information


Unique identifier OMICS_14780
Name matchprobes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.14.1
Stability Stable
Requirements
Biobase, Affy
Maintained Yes

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Maintainer


  • person_outline Wolfgang Huber <>

Publication for matchprobes

matchprobes in publications

 (10)
PMCID: 4460634
PMID: 25971253
DOI: 10.1186/s12918-015-0165-z

[…] [] and 19 (u133a) samples from gse37317 []. we considered only probe sets that were present in both array types u133a and u133plus2. we combined the u133plus2 samples and the u133a samples using the matchprobes bioconductor package []. we normalized the microarray samples using rma and quantile normalization [] using log2 expression intensities for each probe set. as a summary statistic […]

PMCID: 4366630
PMID: 25798051
DOI: 10.7150/ijms.10735

[…] and microarray processing were reported by roessler et al. , and are available at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse14520. hsp gene expression levels were calculated using the matchprobes package in the r programming environment and the log2 rma-calculated signal intensity was reported. details of the experiment protocols and data processing are available […]

PMCID: 4290566
PMID: 25601191
DOI: 10.1186/s13059-014-0561-5

[…] for preprocessing. thus, the robust multi-array average (rma) method was used for background correction. quantile normalization was then done. we also introduced a specific step for pm (perfect matchprobes) adjustment, using the pm-only model-based expression index (option ‘pmonly’). finally, for the summarization step, the median polish method was used. next, variance filtering by iqr […]

PMCID: 3404966
PMID: 22848594
DOI: 10.1371/journal.pone.0041770

[…] genechip hg-u133plus2. we normalized and combined information across different platforms using the standard functions provided by bioconductor packages. we used the combineaffybatch function in the matchprobes library to merge data from hg-u133a and hg-u133plus2 genechips and we applied rma normalization to the merged dataset. the mirna expression profiling panel was performed by integragen […]

PMCID: 3321022
PMID: 22493692
DOI: 10.1371/journal.pone.0034460

[…] mas's work at http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=gse14323. the data from the two affymetrix platforms, hg-u133a and hg-u133a 2.0, were combined by means of the r package matchprobes . the robust multi-array (rma) method was utilized to process the data . duplicated probes for each gene were averaged and the processed data were normalized with the quantile method . […]


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matchprobes institution(s)
Department of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany; Department of Biostatistical Science, Dana Farber Cancer Institute, Boston, MA, USA

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