Currently methods allowing for isolation of SINE and LINE from an unknown genome mostly depend on construction of genomic library and subsequently screening by colony hybridization method using probe specific to particular region of repeated elements.
Genome-based DNA microarrays, an intermediate between non-sequence-based and sequence-based methods, contain probes specific for some or all genes present in a genome [ 41].
The first method used Southern blotting with a subtelomeric probe specific to chromosome 7.
The results suggest that this method may provide a relative simple and reliable way to probe specific interactions between biological molecules.
We could confirm that the polynomial based probe specific correction (PPC) was the most accurate method for allele frequency estimation.
The raw data files underwent background correction, normalization, probe specific correction, and summary value computation using the Robust Multichip Average (RMA) method in the Bioconductor package.
For one-channel array (Affymetrix), MAS 5.0 method provided by the R package, affy, for the Affymetrix rice array was used to conduct background correction, normalization, probe specific background correction, probe summarization and convert probe level data to expression values (Affymetrix[2012]).
Using a previously described method [ 18], inhouse probes specific for FGFR1 were generated and we set out to characterise the prevalence of FGFR1 amplification in a large community-based cohort of breast cancers and its correlations with traditional clinicopathological features, immunohistochemical markers, and disease-free and overall survival.
The methods based on probe-specific p-value summaries (KM, FM, SM, MTS, TS) all produced similar results (p-values between 0.01 and 0.03).
The scanning probe methods yielded specific information, and tapping-mode AFM has shown up to 13-nm-high large-area protrusions not seen in the contact-mode AFM.
