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

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