Question: Query related to topGene functionality in RankProd library.
9.5 years ago by
Fangxin Hong • 20
Fangxin Hong • 20 wrote:
Hi Rohan, Please see my comments below, > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- >> bounces at stat.math.ethz.ch] On Behalf Of Rohan M >> Sent: Monday, December 07, 2009 6:55 AM >> To: bioconductor at stat.math.ethz.ch >> Subject: [BioC] Query related to topGene functionality in RankProd >> library. >> >> 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? >> Theoretically this shouldn't happen as expression level is suppressed when downregulated. I don't know what cutoff point you selected for topGene. If you use a loose criteria, which would lead to gene with not strong signal being identified out, this would happen. For example, if gene A has 4 fold-change readout (in one-channel case) as 1.6,0.9,0.7,0.9 then the average fold-change is1.025. However, this gene might be identified in downregulation list as 3 out of 4 fold changes are less than 1. 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? >> This type result would very much indicate this gene doesn't have decent signal in either direction. This would happen when random variation gives fake signal in both direction, when For example, a gene with 4 fold-changes of 1.3, 0.6, 0.9, 1.2 would results in both list if a loose cut-off point is selected. >> 3) Sometime I see "Inf" as fold change value - must be infinity. Is it >> possible to have such value? >> If there is 0 or negative value in the expression data (like the one normalized with MAS5), then it is possible. As stated in package manual, it is always a good to look at the data when such results coming out, which would help a lot in term of selecting cut-off point and interpret results Hope this would help, let me know if this is not clear or you prefer to send over your data for mt to take a look. Best, Fangxin >> Could you please help me understanding the above points? >> >> Thanks and regards, >> Rohan >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- Fangxin Hong Ph.D. Research Scientist Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute, Harvard School of Public Health Phone: 617-632-3602 Email: fxhong at jimmy.harvard.edu
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