topGene: topGene

Description Usage Arguments Value Author(s) References See Also Examples

Description

Indentify diiffentially expressed genes using rank product method

Usage

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topGene(x,cutoff=NULL,method="pfp",num.gene=NULL,logged=TRUE,
                    logbase=2,gene.names=NULL)

Arguments

x

the value returned by function RP, RPadvance, RSadvance, RankProducts or RP.advance

cutoff

The pfp threshold value used to select genes

method

if cutoff is provided, the method needs to be selected to identify genes. "pfp" uses percentage of false prediction, which is a default setting. "pval" uses p-values which is less stringent than pfp

logged

if "TRUE", data has been logged, otherwise set it to "FALSE"

logbase

base used when taking log, used to restore the fold change.The default value is 2, this will be ignored if logged=FALSE

gene.names

if "NULL", no gene name will be attached to the output table

num.gene

number of candidates genes of interests, if cutoff is provided, this will be ignored

Value

Two tables of identified genes with gene.index: index of gene in the original data set RP/Rsum: Computed rank product/sum for each gene FC:(class1/class2): Expression Fold change of class 1/ class 2. pfp: estimated pfp for each gene if the gene is used as cutoff point P.value: estimated p-value for each gene Table 1 list genes that are up-regulated under class 2, Table 1 ist genes that are down-regulated under class 2

Author(s)

Fangxin Hong [email protected]

References

Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P.(2004) Rank Products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments, FEBS Letter, 57383-92

See Also

plotRP RP RPadvance RSadvance

Examples

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# Load the data of Golub et al. (1999). data(golub)
# contains a 3051x38 gene expression
# matrix called golub, a vector of length called golub.cl
# that consists of the 38 class labels,
# and a matrix called golub.gnames whose third column
# contains the gene names.
data(golub)

#use a subset of data as example, apply the rank
#product method
subset <- c(1:4,28:30)
#Setting rand=123, to make the results reproducible,

#identify genes
RP.out <- RP(golub[,subset],golub.cl[subset],rand=123)

#get two lists of differentially expressed genes
#by setting FDR (false discivery rate) =0.05

table=topGene(RP.out,cutoff=0.05,method="pfp",logged=TRUE,logbase=2,
                gene.names=golub.gnames[,3])
table$Table1
table$Table2

#using pvalue<0.05
topGene(RP.out,cutoff=0.05,method="pval",logged=TRUE,logbase=2,
        gene.names=golub.gnames[,3])

#by selecting top 10 genes
topGene(RP.out,num.gene=10,gene.names=golub.gnames[,3])

Example output

Loading required package: Rmpfr
Loading required package: gmp

Attaching package: 'gmp'

The following objects are masked from 'package:base':

    %*%, apply, crossprod, matrix, tcrossprod

C code of R package 'Rmpfr': GMP using 64 bits per limb


Attaching package: 'Rmpfr'

The following objects are masked from 'package:stats':

    dbinom, dnorm, dpois, pnorm

The following objects are masked from 'package:base':

    cbind, pmax, pmin, rbind

Rank Product analysis for unpaired case 
 

 done  Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

                 gene.index RP/Rsum FC:(class1/class2)     pfp   P.value
HG2724-HT2820_at        418   8.143             0.2689 0.05659 0.0001132
D87116_at               346   8.320             0.2605 0.03057 0.0001223
HG3494-HT3688_at        436   8.653             0.2369 0.02345 0.0001407
                        gene.index RP/Rsum FC:(class1/class2)     pfp   P.value
AFFX-HUMRGE/M10098_3_at          6   6.768              4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at          5   9.967              3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at          4  10.780              4.034 0.05054 3.032e-04
AFFX-M27830_5_at                14  10.800              3.252 0.03811 3.049e-04
Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

$Table1
                         gene.index RP/Rsum FC:(class1/class2)     pfp
HG2724-HT2820_at                418   8.143             0.2689 0.05659
D87116_at                       346   8.320             0.2605 0.03057
HG3494-HT3688_at                436   8.653             0.2369 0.02345
D88422_at                       378  12.810             0.2684 0.06752
HG987-HT987_at                  475  13.740             0.3031 0.06802
D87433_at                       350  18.810             0.3543 0.15400
D26579_at                       141  28.470             0.3970 0.45540
D10495_at                        68  29.680             0.4748 0.44870
D26308_at                       140  32.940             0.5013 0.53580
D30755_at                       160  33.830             0.5308 0.51940
J03909_at                       496  34.260             0.4730 0.48920
D50663_at                       219  35.980             0.5953 0.51340
AFFX-HUMTFRR/M11507_3_at         13  37.430             0.5117 0.52780
D50915_at                       229  38.430             0.6938 0.52660
D89052_at                       381  39.490             0.4630 0.52890
HG620-HT620_at                  470  42.080             0.5305 0.58710
D29643_at                       155  43.170             0.5360 0.59130
AFFX-HUMTFRR/M11507_M_at         12  45.720             0.5309 0.64830
D00726_at                        62  45.790             0.5530 0.61680
D83735_at                       303  49.060             0.6354 0.69860
D26129_at                       139  51.670             0.5489 0.75770
D79996_at                       280  52.420             0.6162 0.74960
HG2788-HT2896_at                419  53.730             0.5948 0.76190
D14874_at                       108  53.760             0.5693 0.73110
HG4662-HT5075_at                466  55.400             0.5835 0.75500
HG3286-HT3463_at                431  56.220             0.5563 0.75200
D87937_at                       374  56.960             0.6749 0.74710
D00761_at                        64  57.480             0.6040 0.73630
HG2810-HT2921_at                420  58.280             0.6070 0.73460
J03040_at                       483  59.410             0.6112 0.74290
D10202_at                        67  59.550             0.5783 0.72300
D86973_at                       333  60.320             0.8143 0.72170
D49817_at                       215  60.620             0.5280 0.70810
AF010193_at                      52  60.850             0.6096 0.69310
                           P.value
HG2724-HT2820_at         0.0001132
D87116_at                0.0001223
HG3494-HT3688_at         0.0001407
D88422_at                0.0005401
HG987-HT987_at           0.0006802
D87433_at                0.0018470
D26579_at                0.0063750
D10495_at                0.0071790
D26308_at                0.0096450
D30755_at                0.0103900
J03909_at                0.0107600
D50663_at                0.0123200
AFFX-HUMTFRR/M11507_3_at 0.0137200
D50915_at                0.0147400
D89052_at                0.0158700
HG620-HT620_at           0.0187900
D29643_at                0.0201100
AFFX-HUMTFRR/M11507_M_at 0.0233400
D00726_at                0.0234400
D83735_at                0.0279400
D26129_at                0.0318200
D79996_at                0.0329800
HG2788-HT2896_at         0.0350500
D14874_at                0.0350900
HG4662-HT5075_at         0.0377500
HG3286-HT3463_at         0.0391000
D87937_at                0.0403500
D00761_at                0.0412300
HG2810-HT2921_at         0.0426000
J03040_at                0.0445800
D10202_at                0.0448300
D86973_at                0.0461900
D49817_at                0.0467300
AF010193_at              0.0471300

$Table2
                        gene.index RP/Rsum FC:(class1/class2)     pfp   P.value
AFFX-HUMRGE/M10098_3_at          6   6.768              4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at          5   9.967              3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at          4  10.780              4.034 0.05054 3.032e-04
AFFX-M27830_5_at                14  10.800              3.252 0.03811 3.049e-04
D88270_at                      377  12.630              3.535 0.05163 5.163e-04
D11086_at                       74  25.340              2.362 0.37840 4.541e-03
D50918_at                      232  28.680              2.485 0.46510 6.511e-03
HG1078-HT1078_at               389  29.320              2.255 0.43330 6.933e-03
D83776_at                      304  36.770              2.114 0.72640 1.308e-02
HG4036-HT4306_at               451  36.840              2.104 0.65690 1.314e-02
D86479_at                      323  38.990              2.083 0.69680 1.533e-02
D86983_at                      337  39.860              1.952 0.67780 1.627e-02
D87465_at                      369  42.420              1.829 0.73840 1.920e-02
D83780_at                      306  43.320              1.987 0.72460 2.029e-02
D42053_at                      193  45.720              1.926 0.77800 2.334e-02
D30742_at                      159  48.730              2.061 0.85860 2.748e-02
AFFX-HSAC07/X00351_3_st         17  50.590              1.981 0.88800 3.019e-02
D78012_at                      267  51.560              1.800 0.87950 3.166e-02
D83785_at                      309  54.710              1.610 0.96390 3.663e-02
HG1612-HT1612_at               394  54.850              1.853 0.92110 3.685e-02
D86970_at                      330  55.590              1.897 0.90630 3.807e-02
D63880_at                      259  56.580              1.753 0.90250 3.971e-02
D63486_at                      248  56.750              1.891 0.86960 4.000e-02
J03600_at                      491  57.810              1.610 0.87090 4.180e-02
D86967_at                      329  57.900              2.127 0.83930 4.196e-02
D87076_at                      344  59.890              2.068 0.87360 4.543e-02
D83783_at                      307  60.980              1.714 0.87720 4.737e-02
HG3039-HT3200_at               425  61.820              1.724 0.87300 4.889e-02

Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

$Table1
                 gene.index RP/Rsum FC:(class1/class2)     pfp   P.value
HG2724-HT2820_at        418   8.143             0.2689 0.05659 0.0001132
D87116_at               346   8.320             0.2605 0.03057 0.0001223
HG3494-HT3688_at        436   8.653             0.2369 0.02345 0.0001407
D88422_at               378  12.810             0.2684 0.06752 0.0005401
HG987-HT987_at          475  13.740             0.3031 0.06802 0.0006802
D87433_at               350  18.810             0.3543 0.15400 0.0018470
D26579_at               141  28.470             0.3970 0.45540 0.0063750
D10495_at                68  29.680             0.4748 0.44870 0.0071790
D26308_at               140  32.940             0.5013 0.53580 0.0096450
D30755_at               160  33.830             0.5308 0.51940 0.0103900

$Table2
                        gene.index RP/Rsum FC:(class1/class2)     pfp   P.value
AFFX-HUMRGE/M10098_3_at          6   6.768              4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at          5   9.967              3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at          4  10.780              4.034 0.05054 3.032e-04
AFFX-M27830_5_at                14  10.800              3.252 0.03811 3.049e-04
D88270_at                      377  12.630              3.535 0.05163 5.163e-04
D11086_at                       74  25.340              2.362 0.37840 4.541e-03
D50918_at                      232  28.680              2.485 0.46510 6.511e-03
HG1078-HT1078_at               389  29.320              2.255 0.43330 6.933e-03
D83776_at                      304  36.770              2.114 0.72640 1.308e-02
HG4036-HT4306_at               451  36.840              2.104 0.65690 1.314e-02

RankProd documentation built on Nov. 17, 2017, 8:51 a.m.