Sentence examples for microarray probe intensities from inspiring English sources
Two of the 17 samples, Mex-1225 and Mex-730, exhibited very weak microarray probe intensities on Virochip analysis and were grouped with the negative control samples.
A comparison between microarray probe intensities and qPCR fold changes indicated that different miRNAs had different levels of correlation, varying from R2 = 0.81 to R2 = 0.95.
Correlation coefficients of microarray probe intensities between biological duplicates were greater than 0.93.
However, the correlation between RNA sequencing reads and microarray probe intensities tends to be quite reasonable [ 27] so major changes seem unlikely.
Affymetrix microarray probe intensities were normalised using RMA normalisation via the Bioconductor/R package oligo (version 1.18.1) (Carvalho and Irizarry, 2010) and differences tested using the Bioconductor/R package limma (version 3.10.3) (Smyth, 2004).
For example, while many microarray probe intensities overestimate gene expression levels by several orders of magnitude, SSMIs for nearly all probes much more closely match TPM values determined by RNA-Seq.
Next, we describe software called "GenePool," which directly analyzes SNP microarray probe intensity data and ranks SNPs by increased likelihood of being genetically associated with a trait or disorder.
We verified expression of PTPN11, SOS1, and SHOC2 mRNA in our samples by checking microarray probe signal intensities for PTPN11 and SOS1, and quantitative real-time PCR signals for SHOC2 that was not represented on the arrays (Supp. Fig. S2).
For these data the most effective was a quantile-based approach, where we identified the 5th and 95th quantile of expression for each microarray probe (using intensity) and for the corresponding RNA-Seq gene (using TPM), and then linearly scaled the microarray intensities so that these values align with TPMs.
As part of this study we also introduce a new pre-processing method of microarray probe set intensity values that helps with the inspection of microarray quality and aides the choice of background compensation and normalization procedure.
The microarray probe set signal intensities had been normalized to a median of 100 [17]; therefore, more than 60% of the 3,678 Arabidopsis nectary-expressed orthologs had signal intensities greater than the median.
