Sentence examples for file probe from inspiring English sources

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.

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].

Probes targeting candidate division TM7 were positive in 40% of the samples; the probes targeting the domain Archaea (Additional file 4: probe o1311, designed to target Crenarchaeota, Class Thermoprotei) were positive in 44% of the samples.

After applying the mask file, only probe sets with at least seven remaining probes were retained for further analysis (n = 18,631).

Additional file 1: Probe handle controls.

Additional file 6: Probe sets of 51-gene signature of stromal activation in primary tumor.

(CSV 1 kb) Additional file 7: Probe IDs used in this study as in the Medicago gene atlas.

The 70 experiments in the dataset are also listed in the Additional file 8. ATH1 probe set-to-Locus ID mapping was obtained from TAIR [ 114, 115].

The script can parse a text file, extract probe and sequence ids (even from fasta-style description lines), connect to the ArrayGene database and find the Entrez Gene id for each probe.

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).