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
Stability Stable
Maintained Yes

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LPE citations

 (4)
2012
PMCID: 3461006

[…] was checked for parameters such as uniform background and foreground intensities over the entire array. the raw signal was background corrected using the normexp method [87] and the arrays were then lowess normalized individually (“normalizewithinarrays” option), with differential weights assigned to probes and to positive control spike-ins, which are expected to show no fold change [88]. […]

2012
PMCID: 3443458

[…] the array quality was assessed by checking for uniform background and foreground intensities over the entire array. the signal was background corrected using the normexp method [62]. the arrays were lowess normalized individually (“normalizewithinarrays” option), with differential weights assigned to probes and to positive control spike-ins, which are expected to show no fold change [63]. […]

2008
PMCID: 2572629

[…] and scanned using a perkin elmer scanarray express scanner., feature intensities for the ra time course were extracted from the scanned image using perkinelmer scanarray software with the default lowess normalization settings; for melan-a vs. b16 comparisons, intensities were extracted using imagene software (biodiscovery, el segundo, ca). all extracted data were exported to microsoft excel […]

2007
PMCID: 1829400

[…] satured spots, the results files were normalized with the in-house developed software arraynorm [56]. after background correction the data sets were normalized by global-mean and dye-swap pairs or lowess-subgrid normalization. the obtained result files were used for further analyses such as cluster analysis [57], go annotation [58] and pathway analyses [59]. cluster analyses were performed […]

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