hello, Thank you very much .I think I should work harder. Thanks again Yuduan Ding 2009-09-25£¬cstrato <cstrato@aon.at>£º >Dear Yuduan Ding, > >Please have a look at the help files "?UniFilter" and "?fcFilter". You >will see that "foldchange=c(1.3, "both")" means that you want to select >"both" up- and down-regulated genes with a foldchange value greater than >1.3 (fc >= 1.3) or less than -1.3 (fc <= -1.3 = -1.0/0.77) Thus >fc=0.702853 is equal to fc=-.1.42. > >Regarding the p-value please note that for this example I have used >"pval<=0.1" and not "pval<=0.01". > >Christian >_._._._._._._._._._._._._._._._._._ >C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a >V.i.e.n.n.a A.u.s.t.r.i.a >e.m.a.i.l: cstrato at aon.at >_._._._._._._._._._._._._._._._._._ > > >yuduanding wrote: >> Hello, >> When I read XPS Vignette "Introduction to the xps Package: Overview"(April, 2009) . I threw into great confusion about something on page18 . >> These is: >> >>> unifltr <- UniFilter(foldchange = c(1.3, "both"), unifilter = c(0.1, "pval")) >>> rma.ufr <- unifilter(data.rma, "tmpdt_Test3Unifilter", getwd(), >>> >> + unifltr, group = c("GrpA", "GrpA", "GrpB", "GrpB"), xps.fltr = rma.pfr, >> + verbose = FALSE) >> The resulting data can be extracted as data.frame: >> >>> tmp <- validData(rma.ufr) >>> tmp >>> >> UNIT_ID Statistics Mean1 Mean2 StandardError >> AFFX-Ce_Gapdh_5_s_at 40 7.06687 298.668 209.920 0.0719846 >> rrlG_b2589_s_at 186 -10.74160 122.945 169.814 0.0433769 >> 37189_at 214 -8.24096 241.766 369.666 0.0743373 >> AFFX-18SRNAMur/X00686_3_at 243 -7.66081 452.422 666.802 0.0730458 >> AFFX-hum_alu_at 277 -63.55890 674.325 5368.190 0.0470889 >> AFFX-HUMISGF3A/M97935_MA_at 283 -15.41420 341.779 458.275 0.0274521 >> AFFX-HUMRGE/M10098_5_at 286 -26.88740 149.584 199.014 0.0153200 >> AFFX-HUMRGE/M10098_M_at 287 -17.77530 125.175 176.651 0.0279579 >> AFFX-MurFAS_at 298 -7.14193 163.431 226.340 0.0657826 >> DegreeOfFreedom P-Value P-Adjusted FoldChange >> AFFX-Ce_Gapdh_5_s_at 1.19543 0.06399260 0.06399260 0.702853 >> rrlG_b2589_s_at 1.49189 0.02160840 0.02160840 1.381220 >> 37189_at 1.00864 0.07560790 0.07560790 1.529020 >> AFFX-18SRNAMur/X00686_3_at 1.05823 0.07425470 0.07425470 1.473850 >> AFFX-hum_alu_at 1.06781 0.00766898 0.00766898 7.960830 >> AFFX-HUMISGF3A/M97935_MA_at 1.61801 0.00952405 0.00952405 1.340850 >> AFFX-HUMRGE/M10098_5_at 1.00504 0.02329990 0.02329990 1.330450 >> AFFX-HUMRGE/M10098_M_at 1.04887 0.03139930 0.03139930 1.411240 >> AFFX-MurFAS_at 1.96059 0.02008720 0.02008720 1.384930 >> The data show that only 9 genes of the pre¡§Cselected 181 genes are considered to be differentially expressed. >> >> Only genes satisfying both filters are considered to be differentially expressed(foldchange>= 1.3&pval <= 0.1)) >> If tmp are considered to be differentially expressed,why some probes have a lower FoldChange Values (like AFFX-Ce_Gapdh_5_s_at 0.702853) >> and higher P-values (like 0.06399260 0.02160840 )? >> thank you! >> Yuduan Ding >> >> [[alternative HTML version deleted]] >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]