geNorm: Ranks genes
In ctrlGene: Assess the Stability of Candidate Housekeeping Genes
Description
Usage
Arguments
Value
References
Examples
Description
Uses the geNorm algorithm to determine the most stably expressed genes.
Usage
1
2
geNorm(expression, genes = data.frame(Genes = character(0), Avg.M =
numeric(0)), ctVal = TRUE)
Arguments
expression
a matrix of expression levels. Each row corresponds to a sample and each column to a gene.
genes
a data frame to output the result of the function
ctVal
a logical value indicating data type. If ct-values are input, ctVal=TRUE, otherwise, ctVal=FALSE.
Value
A sorted dataframe with two columns, 'Genes' and 'Avg.M'. The last two genes are the two most stable control genes.
Avg.M is average expression stability values (M) of remaining control genes during stepwise exclusion of the least stable control gene.
References
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) <doi: 10.1186/gb-2002-3-7-research0034>.
Examples
1
2
3
4
Example output
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA
FIB1 0.4993028 0.3278251 0.5162567 0.3056248 0.4829056 0.3355779 0.3939143
FIB2 0.2387128 0.4780923 0.2877965 0.1156613 0.3138990 0.2395113 0.2509738
FIB3 0.2621082 0.4780923 0.1609739 0.0894386 0.1475879 0.2728241 0.2411161
FIB4 0.1510783 1.0000000 0.4623917 0.2081702 0.2849279 0.2774173 0.3759233
FIB5 0.6788595 0.5999617 0.6949141 0.3344593 0.7655722 0.5821997 0.5537572
FIB6 0.0001598 0.0014965 0.0011456 0.0059427 0.0007649 0.0015524 0.0009345
FIB7 0.5744752 0.5900280 0.4877674 0.3587541 0.5128205 0.4354185 0.4383361
FIB8 0.1839765 0.4845208 0.1927812 0.0772178 0.1515836 0.6328872 0.1344145
FIB9 0.2811475 0.5861008 0.3939143 0.1380535 0.3861008 0.4780923 0.3809781
FIB10 0.0055034 0.0128093 0.0119020 0.0061445 0.0093898 0.0203071 0.0162363
FIB11 0.0081068 0.0232089 0.0168437 0.0168437 0.0137397 0.0485449 0.0424753
FIB12 0.0143014 0.0242386 0.0110590 0.0085517 0.0119020 0.0311365 0.0392042
FIB13 0.0071408 0.0146886 0.0084383 0.0074575 0.0096763 0.0173576 0.0199709
FIB14 0.6972384 0.4472067 0.5939816 0.4926782 0.6244902 0.5391604 0.5556093
FIB15 0.1966825 0.1300003 0.2839780 0.1248942 0.2181329 0.2995626 0.2088665
FIB16 0.4239411 0.0946625 0.5725601 0.3322331 0.5445885 0.3952318 0.3939143
FIB17 0.9900326 0.7209133 0.7209133 0.6328872 0.8778964 0.5249484 0.8808327
FIB18 0.5043297 0.5320069 0.5145358 0.4577828 0.5337864 0.5959683 0.4532199
FIB19 1.0000000 0.7257439 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
FIB20 0.3160023 0.2247878 0.3992109 0.2543484 0.2839780 0.2965767 0.3835309
TBP UBC YWHAZ
FIB1 0.4383361 0.4472067 0.5725601
FIB2 0.2363335 0.2218053 0.3516380
FIB3 0.1864502 0.1779347 0.3066470
FIB4 0.1152758 0.3721764 0.2218053
FIB5 0.8022109 0.5725601 0.8519060
FIB6 0.0000962 0.0003768 0.0006896
FIB7 0.5725601 0.4183163 0.6856942
FIB8 0.1085513 0.1815355 0.1698080
FIB9 0.3278251 0.4113902 0.3423690
FIB10 0.0089013 0.0103101 0.0123473
FIB11 0.0110590 0.0225218 0.0238373
FIB12 0.0137397 0.0177089 0.0154431
FIB13 0.0060428 0.0105892 0.0142063
FIB14 0.5574677 0.5500713 0.7089770
FIB15 0.1876996 0.4457159 0.2347604
FIB16 0.2764925 0.4141468 0.5284659
FIB17 0.8350080 0.8808327 0.9834429
FIB18 0.5077090 0.5900280 0.4670470
FIB19 1.0000000 1.0000000 1.0000000
FIB20 0.3355779 0.4412732 0.3492975
Genes Avg.M
1 HMBS 0.8318952
2 B2M 0.7579472
3 RPL13A 0.6746222
4 SDHA 0.6152281
5 TBP 0.5704086
6 ACTB 0.5215777
7 UBC 0.4263280
8 YWHAZ 0.3646710
9 GAPD-HPRT1 0.2770064
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
FIB1 19.00201 19.60900 18.95384 19.71017 19.05019 19.57528 19.34405 19.18989
FIB2 20.06665 19.06464 19.79688 21.11202 19.67163 20.06183 19.99439 20.08110
FIB3 19.93177 19.06464 20.63510 21.48296 20.76035 19.87396 20.05220 20.42314
FIB4 20.72663 18.00000 19.11281 20.26416 19.81133 19.84987 19.41149 21.11684
FIB5 18.55882 18.73706 18.52509 19.58010 18.38539 18.78041 18.85267 18.31795
FIB6 30.61144 27.38419 27.76968 25.39467 28.35244 27.33128 28.06352 31.34360
FIB7 18.79968 18.76114 19.03573 19.47893 18.96347 19.19953 19.18989 18.80450
FIB8 20.44241 19.04537 20.37496 21.69492 20.72181 18.65998 20.89524 21.20355
FIB9 19.83060 18.77078 19.34405 20.85670 19.37295 19.06464 19.39222 19.60900
FIB10 25.50546 24.28666 24.39265 25.34649 24.73469 23.62187 23.94463 24.81177
FIB11 24.94665 23.42918 23.89165 23.89165 24.18551 22.36454 22.55723 24.49864
FIB12 24.12770 23.36655 24.49864 24.86957 24.39265 23.00525 22.67285 24.18551
FIB13 25.12970 24.08916 24.88883 25.06709 24.69133 23.84829 23.64596 25.37057
FIB14 18.52028 19.16099 18.75151 19.02128 18.67925 18.89121 18.84786 18.84304
FIB15 20.34606 20.94341 19.81615 21.00122 20.19672 19.73907 20.25935 20.41350
FIB16 19.23806 21.40106 18.80450 19.58973 18.87676 19.33923 19.34405 19.85469
FIB17 18.01445 18.47210 18.47210 18.65998 18.18788 18.92975 18.18306 18.26014
FIB18 18.98756 18.91048 18.95866 19.12726 18.90567 18.74669 19.14172 18.97793
FIB19 18.00000 18.46247 18.00000 18.00000 18.00000 18.00000 18.00000 18.00000
FIB20 19.66199 20.15336 19.32478 19.97512 19.81615 19.75352 19.38259 19.57528
UBC YWHAZ
FIB1 19.16099 18.80450
FIB2 20.17263 19.50784
FIB3 20.49058 19.70535
FIB4 19.42594 20.17263
FIB5 18.80450 18.23123
FIB6 29.37391 28.50195
FIB7 19.25733 18.54436
FIB8 20.46168 20.55802
FIB9 19.28142 19.54638
FIB10 24.59980 24.33966
FIB11 23.47253 23.39064
FIB12 23.81938 24.01689
FIB13 24.56126 24.13733
FIB14 18.86231 18.49619
FIB15 19.16580 20.09074
FIB16 19.27179 18.92012
FIB17 18.18306 18.02409
FIB18 18.76114 19.09836
FIB19 18.00000 18.00000
FIB20 19.18026 19.51747
Genes Avg.M
1 HMBS 0.8318952
2 B2M 0.7579472
3 RPL13A 0.6746222
4 SDHA 0.6152281
5 TBP 0.5704086
6 ACTB 0.5215777
7 UBC 0.4263280
8 YWHAZ 0.3646710
9 GAPD-HPRT1 0.2770064
ctrlGene documentation built on July 4, 2019, 5:05 p.m.
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Description Usage Arguments Value References Examples
Description
Uses the geNorm algorithm to determine the most stably expressed genes.
Usage
1 2 | geNorm(expression, genes = data.frame(Genes = character(0), Avg.M =
numeric(0)), ctVal = TRUE)
|
Arguments
expression |
a matrix of expression levels. Each row corresponds to a sample and each column to a gene. |
genes |
a data frame to output the result of the function |
ctVal |
a logical value indicating data type. If ct-values are input, ctVal=TRUE, otherwise, ctVal=FALSE. |
Value
A sorted dataframe with two columns, 'Genes' and 'Avg.M'. The last two genes are the two most stable control genes.
Avg.M is average expression stability values (M) of remaining control genes during stepwise exclusion of the least stable control gene.
References
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) <doi: 10.1186/gb-2002-3-7-research0034>.
Examples
1 2 3 4 |
Example output
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA
FIB1 0.4993028 0.3278251 0.5162567 0.3056248 0.4829056 0.3355779 0.3939143
FIB2 0.2387128 0.4780923 0.2877965 0.1156613 0.3138990 0.2395113 0.2509738
FIB3 0.2621082 0.4780923 0.1609739 0.0894386 0.1475879 0.2728241 0.2411161
FIB4 0.1510783 1.0000000 0.4623917 0.2081702 0.2849279 0.2774173 0.3759233
FIB5 0.6788595 0.5999617 0.6949141 0.3344593 0.7655722 0.5821997 0.5537572
FIB6 0.0001598 0.0014965 0.0011456 0.0059427 0.0007649 0.0015524 0.0009345
FIB7 0.5744752 0.5900280 0.4877674 0.3587541 0.5128205 0.4354185 0.4383361
FIB8 0.1839765 0.4845208 0.1927812 0.0772178 0.1515836 0.6328872 0.1344145
FIB9 0.2811475 0.5861008 0.3939143 0.1380535 0.3861008 0.4780923 0.3809781
FIB10 0.0055034 0.0128093 0.0119020 0.0061445 0.0093898 0.0203071 0.0162363
FIB11 0.0081068 0.0232089 0.0168437 0.0168437 0.0137397 0.0485449 0.0424753
FIB12 0.0143014 0.0242386 0.0110590 0.0085517 0.0119020 0.0311365 0.0392042
FIB13 0.0071408 0.0146886 0.0084383 0.0074575 0.0096763 0.0173576 0.0199709
FIB14 0.6972384 0.4472067 0.5939816 0.4926782 0.6244902 0.5391604 0.5556093
FIB15 0.1966825 0.1300003 0.2839780 0.1248942 0.2181329 0.2995626 0.2088665
FIB16 0.4239411 0.0946625 0.5725601 0.3322331 0.5445885 0.3952318 0.3939143
FIB17 0.9900326 0.7209133 0.7209133 0.6328872 0.8778964 0.5249484 0.8808327
FIB18 0.5043297 0.5320069 0.5145358 0.4577828 0.5337864 0.5959683 0.4532199
FIB19 1.0000000 0.7257439 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
FIB20 0.3160023 0.2247878 0.3992109 0.2543484 0.2839780 0.2965767 0.3835309
TBP UBC YWHAZ
FIB1 0.4383361 0.4472067 0.5725601
FIB2 0.2363335 0.2218053 0.3516380
FIB3 0.1864502 0.1779347 0.3066470
FIB4 0.1152758 0.3721764 0.2218053
FIB5 0.8022109 0.5725601 0.8519060
FIB6 0.0000962 0.0003768 0.0006896
FIB7 0.5725601 0.4183163 0.6856942
FIB8 0.1085513 0.1815355 0.1698080
FIB9 0.3278251 0.4113902 0.3423690
FIB10 0.0089013 0.0103101 0.0123473
FIB11 0.0110590 0.0225218 0.0238373
FIB12 0.0137397 0.0177089 0.0154431
FIB13 0.0060428 0.0105892 0.0142063
FIB14 0.5574677 0.5500713 0.7089770
FIB15 0.1876996 0.4457159 0.2347604
FIB16 0.2764925 0.4141468 0.5284659
FIB17 0.8350080 0.8808327 0.9834429
FIB18 0.5077090 0.5900280 0.4670470
FIB19 1.0000000 1.0000000 1.0000000
FIB20 0.3355779 0.4412732 0.3492975
Genes Avg.M
1 HMBS 0.8318952
2 B2M 0.7579472
3 RPL13A 0.6746222
4 SDHA 0.6152281
5 TBP 0.5704086
6 ACTB 0.5215777
7 UBC 0.4263280
8 YWHAZ 0.3646710
9 GAPD-HPRT1 0.2770064
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
FIB1 19.00201 19.60900 18.95384 19.71017 19.05019 19.57528 19.34405 19.18989
FIB2 20.06665 19.06464 19.79688 21.11202 19.67163 20.06183 19.99439 20.08110
FIB3 19.93177 19.06464 20.63510 21.48296 20.76035 19.87396 20.05220 20.42314
FIB4 20.72663 18.00000 19.11281 20.26416 19.81133 19.84987 19.41149 21.11684
FIB5 18.55882 18.73706 18.52509 19.58010 18.38539 18.78041 18.85267 18.31795
FIB6 30.61144 27.38419 27.76968 25.39467 28.35244 27.33128 28.06352 31.34360
FIB7 18.79968 18.76114 19.03573 19.47893 18.96347 19.19953 19.18989 18.80450
FIB8 20.44241 19.04537 20.37496 21.69492 20.72181 18.65998 20.89524 21.20355
FIB9 19.83060 18.77078 19.34405 20.85670 19.37295 19.06464 19.39222 19.60900
FIB10 25.50546 24.28666 24.39265 25.34649 24.73469 23.62187 23.94463 24.81177
FIB11 24.94665 23.42918 23.89165 23.89165 24.18551 22.36454 22.55723 24.49864
FIB12 24.12770 23.36655 24.49864 24.86957 24.39265 23.00525 22.67285 24.18551
FIB13 25.12970 24.08916 24.88883 25.06709 24.69133 23.84829 23.64596 25.37057
FIB14 18.52028 19.16099 18.75151 19.02128 18.67925 18.89121 18.84786 18.84304
FIB15 20.34606 20.94341 19.81615 21.00122 20.19672 19.73907 20.25935 20.41350
FIB16 19.23806 21.40106 18.80450 19.58973 18.87676 19.33923 19.34405 19.85469
FIB17 18.01445 18.47210 18.47210 18.65998 18.18788 18.92975 18.18306 18.26014
FIB18 18.98756 18.91048 18.95866 19.12726 18.90567 18.74669 19.14172 18.97793
FIB19 18.00000 18.46247 18.00000 18.00000 18.00000 18.00000 18.00000 18.00000
FIB20 19.66199 20.15336 19.32478 19.97512 19.81615 19.75352 19.38259 19.57528
UBC YWHAZ
FIB1 19.16099 18.80450
FIB2 20.17263 19.50784
FIB3 20.49058 19.70535
FIB4 19.42594 20.17263
FIB5 18.80450 18.23123
FIB6 29.37391 28.50195
FIB7 19.25733 18.54436
FIB8 20.46168 20.55802
FIB9 19.28142 19.54638
FIB10 24.59980 24.33966
FIB11 23.47253 23.39064
FIB12 23.81938 24.01689
FIB13 24.56126 24.13733
FIB14 18.86231 18.49619
FIB15 19.16580 20.09074
FIB16 19.27179 18.92012
FIB17 18.18306 18.02409
FIB18 18.76114 19.09836
FIB19 18.00000 18.00000
FIB20 19.18026 19.51747
Genes Avg.M
1 HMBS 0.8318952
2 B2M 0.7579472
3 RPL13A 0.6746222
4 SDHA 0.6152281
5 TBP 0.5704086
6 ACTB 0.5215777
7 UBC 0.4263280
8 YWHAZ 0.3646710
9 GAPD-HPRT1 0.2770064
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