[BioC] About xps Unifiter

[cstrato]

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
>
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>
>   
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