=== qrtpcr_pma_timecourse.tbl.txt.bz2 ##ColumnVariables[id] = primer name ##ColumnVariables[chrom] = The name of the chromosome ##ColumnVariables[start] = The starting position of the cluster in the chromosome. The first base in a chromosome is numbered 1 (conventional 1-based coordinate system) ##ColumnVariables[end] = The ending position of the feature in the chromosome ##ColumnVariables[FWD] = forward primer sequnece ##ColumnVariables[REV] = reverse primer sequence ##ColumnVariables[EntrezGene_id] = EntrezGene ID ##ColumnVariables[EntrezGene_symbol] = gene symbol of the EntrezGene ##ColumnVariables[EntrezGene_synonyms] = synonyms of the EntrezGene ##ColumnVariables[status] = mapping status of the primer pair onto the genome and EntrezGene ##ColumnVariables[norm.RIKEN1_PMA_0h] = normalized copy number at PMA_0h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_1h] = normalized copy number at PMA_1h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_2h] = normalized copy number at PMA_2h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_4h] = normalized copy number at PMA_4h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_6h] = normalized copy number at PMA_6h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_12h] = normalized copy number at PMA_12h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_24h] = normalized copy number at PMA_24h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_48h] = normalized copy number at PMA_48h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_72h] = normalized copy number at PMA_72h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN1_PMA_96h] = normalized copy number at PMA_96h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_0h] = Ct value at PMA_0h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_1h] = Ct value at PMA_1h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_2h] = Ct value at PMA_2h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_4h] = Ct value at PMA_4h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_6h] = Ct value at PMA_6h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_12h] = Ct value at PMA_12h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_24h] = Ct value at PMA_24h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_48h] = Ct value at PMA_48h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_72h] = Ct value at PMA_72h of the biological replicate RIKEN1 ##ColumnVariables[raw.RIKEN1_PMA_96h] = Ct value at PMA_96h of the biological replicate RIKEN1 ##ColumnVariables[norm.RIKEN3_PMA_0h] = normalized copy number at PMA_0h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_1h] = normalized copy number at PMA_1h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_2h] = normalized copy number at PMA_2h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_4h] = normalized copy number at PMA_4h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_6h] = normalized copy number at PMA_6h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_12h] = normalized copy number at PMA_12h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_24h] = normalized copy number at PMA_24h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_48h] = normalized copy number at PMA_48h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_72h] = normalized copy number at PMA_72h of the biological replicate RIKEN3 ##ColumnVariables[norm.RIKEN3_PMA_96h] = normalized copy number at PMA_96h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_0h] = Ct value at PMA_0h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_1h] = Ct value at PMA_1h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_2h] = Ct value at PMA_2h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_4h] = Ct value at PMA_4h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_6h] = Ct value at PMA_6h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_12h] = Ct value at PMA_12h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_24h] = Ct value at PMA_24h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_48h] = Ct value at PMA_48h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_72h] = Ct value at PMA_72h of the biological replicate RIKEN3 ##ColumnVariables[raw.RIKEN3_PMA_96h] = Ct value at PMA_96h of the biological replicate RIKEN3 # # # --------------- # Normalization # --------------- # # 1. Copy number conversion for each gene # # We calculated copy numbers by using coefficients (slope and intercept) # of standard curves which were obtained by using genomic DNA. # # raw copy number = 10 ^ { ( raw Ct value - intercept ) / slope } # # # 2. Invariant Set (IS) # # We looked for genes that retained their ordering across two experimental # samples and considered this subset a rank invariant set. # (Because copy number below 40 is not reliable, we didnt include any # invariant gene that has copy number < 40 in a invariant set.) # # We found rank invariant sets for each possible pairwise combination of # experimental samples within a time course and then took the intersection # of all the invariant sets. # # 3. Scaling for each sample # # We scaled all copy numbers in each sample by the geometric average of # copy number of the genes in the final invariant set. # The scale factor used is a ratio of the 2 geometric averages of copy numbers. # # For sample t, # the scale factor = {geometric average expression of IS in control sample} / {geometric average expression of IS in sample t} # # For gene g in sample t, # normalized copy number = {copy number of gene g in sample t} * {the scale factor of sample t} # # The control sample here is PMA_0_hour #