Finally, all mentioned algorithms get a pixel's array as input and output data structure.
In line 24 of Fig. 5, the nonZeroValues function takes an array as input and returns the same array without zero values, while the size function returns the size of the array.
After stringent microarray data filtering (Supplementary Information S1), 572 of the initial ∼20,000 transcripts on the array remained as input for further analysis (Supplementary Information S1).
However, many algorithms for gene expression analysis, including NCA and PCA, require a complete matrix of gene array values as input.
Other groups have reported analysis of total RNA arrays with input as high as 20 40 ug per microarray, which may have improved the results for our total RNA arrays[ 32] That being said, in real world situations researchers will not have abundant amounts of clinically relevant total RNA to use for comparisons to low-input RNA samples.
In order to statistically test whether gene expression was affected by gene dosage we applied an array CGH expression integration tool, ACE-it[6], in which the called array CGH and normalized log10 ratios for expression arrays were used as input data.
The distributed_data_object supports most of numpy's indexing functionality, so it is possible to work with scalars, tuples, lists, numpy arrays and distributed_data_objects as input data.
The *.CEL files and *.RPT files generated by Affymetrix software from scans of the arrays were used as input.
The techniques involved here are not limited to data from SNP arrays, they require as input only a matrix of hybridization ratios (for the former) or copy number values (for the latter).
Most functions take an image (i.e., a multi-dimensional array) as an input parameter: Optional parameters can be passed as Python keyword arguments, in addition to the image parameter.
