I'm in need for a set of highly expressed constitutive set of genes for an organism of interest. I found microarray data for my organism where they have done whole transcriptome profiling for finding differential expression between two developmental stages of the same organism.
I have downloaded the microarray dataset of my organism from NCBI GEO. I have a file that contains raw data and another file containing log normalized (processed) data of every gene in the organism. The authors in their papers have indicated that genes with log2 normalized ratios between 0.6 and 1.7 are supposed to be the constitutively expressed gene set. The genes lying in the given range can be extracted from the processed data file of log normalized values in these ranges.
But If I have to find highly expressed genes from this whole set of constitutively expressed genes,I require individual intensity of the genes from the raw data so that I can compare and find out highly expressing constitutive genes.
Is there any way to use the log normalized ratios to find absolute signal intensities of that gene? If so, how can it be done? Also, if I can find absolute intensities from the raw data, which column in the raw data file should be chosen?
Thank you for your prompt reply. The experiment was a two condition expt. each of these two conditions labelled by Alexa 647 and Alexa 555 dyes respectively. Though no platform was specifically mentioned, they mentioned in their paper that "The microarrays were printed on SuperChip (Erie Scientific) using a BioRobotics MicroGrid (Genomic solutions Inc, Ann Arbor, MI)." Also the raw data consists of the following columns. The data was processed by GenePix Pro. "Block Column Row Name ID X Y Dia. F647 Median F647 Mean F647 SD F647 CV B647 B647 Median B647 Mean B647 SD B647 CV % > B647+1SD % > B647+2SD F647 % Sat. F555 Median F555 Mean F555 SD F555 CV B555 B555 Median B555 Mean B555 SD B555 CV % > B555+1SD % > B555+2SD F555 % Sat. Ratio of Medians (647/555) Ratio of Means (647/555) Median of Ratios (647/555) Mean of Ratios (647/555) Ratios SD (647/555) Rgn Ratio (647/555) Rgn R2 (647/555) F Pixels B Pixels Circularity Sum of Medians (647/555) Sum of Means (647/555) Log Ratio (647/555) F647 Median - B647 F555 Median - B555 F647 Mean - B647 F555 Mean - B555 F647 Total Intensity F555 Total Intensity SNR 647 SNR 555 Flags Normalize Autoflag ". Now which columns should I choose from the above mentioned column headings? I'm a novice in microarrays and still learning.