Question: Query related to topGene functionality in RankProd library.
9.5 years ago by
Rohan M • 20
Rohan M • 20 wrote:
Dear Sir, I'm using RankProd library to find the significant genes in microarray studies. I'm facing some problems in understanding the output of topGene functionality. Could you help me on following queries? 1) The topGene functionality outputs Table1: Genes called significant under class1 < class2 (Up regulated Genes) and Table2: Genes called significant under class1 > class2 (Down regulated genes). When I see the fold change value in both tables , there are some genes having fold change value less than 1 in Table 1 and some genes have fold change value greater than 1 in Table 2. "If the Gene has fold change value less than 1 then its down regulated" how can I interpret fold change value (up regulated or down regulated ) in such case? 2) In some cases both Table 1 and Table 2 contains same probe. Is it possible to have one probe present in both tables? If Yes, then which one should be considered? 3) Sometime I see "Inf" as fold change value - must be infinity. Is it possible to have such value? Could you please help me understanding the above points? Thanks and regards, Rohan [[alternative HTML version deleted]]
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