Dear Wolfgang,

Thank you for your reply. And, sorry for being late as apparently the
CC- of the replied Email (if there was any) didn't reach my Email
account.

ad 1.: Thank you !

ad 2.: Allow me to put the question this way - had there been one (or,
two) outlier array in Fig 3.2. of the book
(http://tinyurl.com/2ervgpn), what would you expect to see in the
heatmap ?

Would the figure, then, look like the heatmap [of Fig. 1(d)] presented
on the final page of arrayQualityMetrics-paper (while ignoring the
right dendogram so that framework-wise comparison is possible with Fig
3.2])? However, in Fig. 1(d), array 1 looks to be an outlier rather
than array 18, as mentioned in that figure !

greetings,

Chintanu



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Dear Chintanu

ad 1.: the assumption is that the arrays that you compare study similar
biological system, e.g. the same cell line treated with different drugs,
such that the gene expression differences for most genes are relatively
minor. The assumption would not hold if you compare, say, a cow liver to
human glioblastoma.

ad 2.: I am not sure I understand your question, and maybe you need to
precisify it. The heatmap is a data exploration tool, there is no single
right way to read it. For instance, in Fig 3.2. that you pointed to, I'd
say there are three clusters (batches) of arrays, with two of them a bit
more similar to each other than to the third.

	Best wishes
	Wolfgang

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