[BioC] About xps Unifiter
cstrato
cstrato at aon.at
Fri Sep 25 16:38:27 CEST 2009
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]]
>
>
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