Dear Experts,

As I have already posted in other questions I have asked recently, I'm a newbie and I'm working with single-channel array data on small ncRNAs detected with a custom array analyzed through GenePix.

Which diagnostic plots would you recommend for this type of analysis (single-channel)? Would, for example, be useful (or correct for that matter) to apply a plotMD() after background correction and quantile normalization to single case samples compared to a group of control samples? Given that plotMD for EList objects compares a selected array with an average array obtained from all the others, I thought it would be useful to compare single case arrays with the average of the control ones and emulate a plotMD on a dual-channel array after a normalizeWithinArrays(). Is that ok? It seems to me that including other case arrays in the average artificial array plotMD produces for single-channel arrays would not be very informative or appropriate when plotting a MA diagram. What would you recommend otherwise?

Thanks!

~Dario

It's up to you really -- it's your experiment and your data.

The default plotMD() plot for ELists is designed for technical quality assessment. For that purpose, evaluating whether each array agrees with the average of the others is quite appropriate. It picks up whether individual arrays are outliers for some reason.

To plot individual arrays vs the controls, one easy way is:

plotMD(y[,c(i,j)]

where y is the EList, i is the column number of the individual case, and j holds the column numbers of the control arrays.