This function is used to check microarray data quality. It can
check the data within the same array or cross different arrays. Normally, on one array, the intensity data for both channels (Cy5 and Cy3)
should be highly correlated (also apparent on the RI plot). The intensity data
for the same sample on different arrays should be highly correlated
too. Normally if an error happened in gridding, only a few blocks
will be gridded. This function does the scatter plot on a grid basis
to check the quality of hybridization and gridding.
If you only provide array1 (either an integer or a vector), it will do
grid check within the same array, that is, for each slide, there will
be one scatter plot for log2(Red) versus log2(Green) for each grid.
If you provide array1 and array2 (both need to be one integer), it
will check the data for the same sample (sample ID information is in
experimental design) for these two arrays. If there's no common sample
on these two arrays, the function will report an error.
In either case, you should see a nearly linear curve in all
plots. If there were errors in hybridization and/or gridding, some of
the plots will look messy. Then you have to check if something wrong
happened, e.g., miss labeling, wrong gridding, etc.
If you don't have grid information for the data, this function will be
unavailable.
Note that this function only works for 2-dye array.