The guidelines encourage using a checklist to ensure the reporting of important experimental parameters, such as standards used, number and type of replicates, statistics, method of randomization, whether experimenters were blind to the conduct of the experiment, how the sample size was determined, and what criteria were used to include or exclude any data," McNutt wrote.
Using a collection of 1152 neuronally relevant cDNAs, this report describes simple modifications in experimental design of radioactive microarray experiments that, (1) improves reproducibility; (2) allows recovery from a failed experiment and; (3) provides a type of replicate data set with no requirement for additional arrays, no additional probe labelings, and little extra cost.
The flags were used to remember the type of replicates that where part of the merge.
The approach used was to estimate a common correlation for all the genes within blocks corresponding to each type of replicate.
There is yet another type of replicates – multiple array spots that are mapped to different regions of the same gene, thus allowing multiple measurements of the RNA levels in the exact same biological sample on the same array.
The type of replicate affects the statistical model that should be used: When applying statistical tests, technical replicates cannot necessarily be viewed as independent observations, so a more refined statistical analysis, e.g., nested analysis of variance (ANOVA), can give better results (Karp et al. 2005).
Since Sabin poliovirus type 1 was not capable of replicating in THP1 and HL60 cells whereas replication in KG1 cells was efficient, expression levels of CD155 thus cannot fully predict the capacity of Sabin poliovirus type 1 to replicate in these cell lines.
This is supported by recent studies illustrating a balance between growth of xenograft tumours in mice and replication of wild-type adenovirus, resulting in detection of replicating virus 100 days following infection without reduction of the tumour mass (Harrison et al, 2001).
For three or more replicates, using mixed types of replicates is superior even to only using sensitive replicates, coming to within two bans of the IMP.
