Sentence examples for cdf version from inspiring English sources
This annotation is based on the CDF-Merger procedure as described by De Leeuw et al. [ 47], which generates a hybrid CDF based on the standard Affymetrix CDF (version 26) and the custom Brainarray (version 11.0.1) CDF.
Probesets were redefined according to Dai et al. using remapped CDF version 11.0.2 based on the Entrez Gene database [13].
A Custom CDF Version 11 with Entrez based gene definitions was used to annotate the arrays.
Expression levels of probe sets were calculated using Robust Multiarray Averaging (RMA) with m-estimator summarization and remapped in Common Data Format (CDF) version 17.0.1 [ 29].
Data were normalized using the Robust Multi-array Average (RMA) algorithm in R software with the custom chip description file (CDF) version 17.0.0 [ 27].
A number of 1740 probe sets, according to custom CDF version 8 [ 44], corresponding to 935 genes were found to be significantly regulated at a cut-off (negative log10) of 5.5584 (Additional file 1).
Custom CDFs version 8 (UniGene CDF files) [ 44] were used for annotations.
Each dataset was preprocessed separately using GCRMA background correction, normalization, and probeset summarization (Wu et al. 2004), with probeset-to-gene mappings provided by BrainArray Custom CDFs (Version 11) (Dai et al. 2005).
Microarrays were normalized using RMA and the University of Michigan custom CDF file (version 12.1.0) with mappings to Ensembl exon IDs.
Probes were summarized according to improved probe definitions (custom CDF hgu133plus2hsensgcdf, version 12) and data were normalized using the robust multiarray (RMA) average expression measure with R/Bioconductor v.2.9.1.
Raw data were RMA robust multi-array analysis background corrected, 17 quantile normalized, 18 and transformed with a logarithm to base 2. Probe sets were mapped and summarized to their respective Ensembl gene ID using custom cdf "HGU133Plus2_Hs_ENSG" version 15.1.0 (downloaded from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/ensg.asp, accessed 9 October 2012).
