I have studied one paper entitled "Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts" . I want to know how the Fold change values calculated in this paper were retrieved. Is there any specific formula available or it was totally determined from software. I have also accessed the required and individual GEO accession(for comparing hypoxia and normoxia data samples as control and diseased samples respectively) available at NCBI-GEO datasets for the same paper. But the value given there is negative LOG FC for upregulated transcripts (based on individual profile transcripts ID). In contrast the value given for upregulated genes in the same paper is positive for upregulated transcripts. I did not get the discrepancy observed in these results. I have also tried to calculate the FC value from individual expression values for each transcript and every unique  accession for normal and hypoxia samples. but the values for FC are totally different from paper data. I want to utilize the microarray data available from GEO for my work. Is there exist any specific method for data processing from such a microarray expression. Please share with me.