Sentence examples for files probe from inspiring English sources

The robust multi array average (RMA) algorithm was implemented to quantify gene expression in GeneSpring version GX7.3 (Agilent, Inc) using either the Affymetrix library file or custom CDF files ("probe masks") that were generated following Hammond et al. [ 89].

In the latter file, probe sets whose consensus sequences mapped to one or no genomic positions receive mapping codes "SM" or "NM" respectively, and probe sets mapping to multiple positions are annotated with code "MM".

After quality assessment and normalization of the arrays, gene-level expression values were derived from the CEL file probe-level hybridization intensities using the model-based Robust Multichip Average algorithm.

Intensities for replicate array measurements were averaged together for each respective tissue, and using the provided annotation files, each probe was mapped to its respective Ensembl gene identifier, and multiple probes matching the same Ensembl gene identifier were averaged together.

Brainarray database has realigned probes to different transcripts, and generated files with probe-clusters that include transcript-specific probes as well as those common to multiple alternatively spliced forms [ 22].

CEL files containing probe intensity data were analysed in R using Bioconductor packages [ 75, 76].

Data analysis used the raw Agilent Feature Extraction data files and probe annotation from GEO.

After scanning the GeneChips, the exported files with probe signal intensities (cel files) were quantile-normalized and background corrected using the affy package from Bioconductor (http://bioconductor.org).

Hereby, result text files containing probe signal and p values for the corresponding oligonucleotides are imported and mapped onto known genes and intergenic regions of P. aeruginosa PAO1.

gDNA: genomic DNA; cel: cell intensity files; cdf: probe mask layout description files; CDF: hybridisation intensity threshold value; EST: Expressed Sequence Tag; GO: Gene Ontology; PM: Perfect Match; BIN: functional gene category code.

A parser script, written in Perl, was developed to generate probe-masking files by removing probe-pairs whose PM probe signal intensity value was below a user-defined gDNA hybridisation intensity threshold.