Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues

BMC Genomics

Table 3 Outcome of linear correction procedure for RNA quality

Brain tissues	Correcting consistent transcripts only		Correcting HG-U133_AB and HG-U133_Plus2.0 data independently		Inter-chip coherence of RNA quality profiles
	Increased	Decreased	Increased	Decreased
Brodmann area 35	684	715	1355	2467	0,67
Caudate nucleus	544	688	1062	2164	0,48
Nucleus ambiguus	849	1367	754	2924	0,79
Nucleus basalis *	1013	526	1690	3089	0,01 *
Pulvinar *	675	442	1301	2401	-0,11 *
Putamen	962	1331	729	3390	0,74
Reticular formation	385	389	865	2329	0,37
Septal area	1185	2698	1175	6587	0,80
Substantia nigra *	685	257	808	1935	-0,13 *
Subthalamic nucleus	588	704	1454	3771	0,43

Number of transcripts with corrected expression profiles exhibiting increase and decrease in inter-platform correlation after linear correction for RNA quality. Linear correction was performed in two variants: 1) correcting profiles which show significant (p < 0.05) RNA quality dependency of the same sign on both chips (consistent transcripts), and 2) correcting all significantly correlated (p < 0.05) to RNA quality profiles in two chips independently. The last column shows coherency of RNA quality profiles for two chip datasets. Sample sets with not correlated RNA quality profiles are marked by asterisk.

ISSN: 1471-2164