Similarly, scores of each gene obtained from animal expression array were assigned by −log10p.
To investigate the activation or repression of specific cellular pathways, genes present on the array were assigned to 25 groups, based on their biological function.
We compared the distribution of p-values for this analysis to ANOVAs for the same partition where each array was assigned to a partition at random.
In Step 6, each gene on the array was assigned to a GO identifier, and a gene set enrichment test was performed to compare P&R vs. P and R vs. P using Limma [ 30, 33].
Using COLONY to reconstruct sibship and parentage by the most accurate method of full-likelihood, we found that 179 seedlings in the 1st SNP array and 188 seedlings in the 2nd SNP array were assigned into 35 and 36 full-sib seed families respectively.
In addition, probe sets of the Affymetrix Medicago genome array were assigned to gene families described in the TAIR database (Rhee et al., 2003) and to transcription factor families provided by the Database of Arabidopsis Transcription Factors [ 30] based on their sequence similarity with Arabidopsis thaliana proteins.
In addition, probe sets of the Affymetrix Medicago Genome Array were assigned to gene families described in the TAIR database [ 95] and to transcription factor families provided by the Database of Arabidopsis Transcription Factors [ 43] based on their sequence similarity with Arabidopsis thaliana proteins.
The selected list would be identical regardless of how arrays are assigned to names in this case.
All RefSeq genes covered by both the expression arrays and the aCGH arrays were assigned expression states and scaffold/matrix association states.
The variable atommap is assigned an array of arrays, [[a1, b1], [a2,b2], ….], indicating the exact 1 1 correlation of these two structures in terms of atom indices.
