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Last data update: 2014.03.03 |
Generate QC stats from an AffyBatch objectDescriptionGenerate QC metrix for Affymetrix data. Usageqc(unnormalised, ...) Arguments
DetailsAffymetrix recommend a series of QC metrics that should be used to check that arrays have hybridised correctly and that sample quality is acceptable. These are discussed in the document 'QC and Affymetrix data' accompanying this package, and on the web at http://bioinformatics.picr.man.ac.uk. They are described in detail in the 'Expression Analysis Fundamentals' manual available from Affymetrix. Before using this function you are strongly encouraged to read the 'QC and Affymetrix data' document, which contains detailed examples. This function takes an Author(s)Crispin J Miller See Also
Examples
## Not run:
qcs <- qc(eset,eset.mas)
## End(Not run)
data(qcs)
ratios(qcs)
avbg(qcs)
maxbg(qcs)
minbg(qcs)
spikeInProbes(qcs)
qcProbes(qcs)
percent.present(qcs)
plot(qcs)
sfs(qcs)
target(qcs)
ratios(qcs)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(simpleaffy)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: affy
Loading required package: genefilter
Loading required package: gcrma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/simpleaffy/qc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: qc
> ### Title: Generate QC stats from an AffyBatch object
> ### Aliases: qc qc,AffyBatch-method
> ### Keywords: misc
>
> ### ** Examples
>
> ## Not run:
> ##D qcs <- qc(eset,eset.mas)
> ##D
> ## End(Not run)
> data(qcs)
> ratios(qcs)
actin3/actin5 actin3/actinM gapdh3/gapdh5
0203_YH10_H_MCF7_r1.CEL 0.08560278 -0.13927277 -0.2882327
0203_YH24_H_MCF7_r2.CEL 0.07697926 -0.19126947 -0.2823266
0203_YH25_H_MCF7_r3.CEL 0.06804130 -0.23387107 -0.2137072
0403_YH35_H_a1MCF7_r1_2.CEL 5.99052862 4.33256971 3.6482383
0403_YH36_H_a1MCF7_r2.CEL 5.81167692 4.92600016 3.7508887
0403_YH37_H_a1MCF7_r3_2.CEL 5.85535460 3.79108521 3.9236571
0203_YH14_H_a10MCF7_r1.CEL 2.79123667 1.58337477 1.4594917
0203_YH19_H_a10MCF7_r2.CEL 2.81536065 1.31413895 1.5801740
0203_YH20_H_a10MCF7_r3.CEL 3.39800077 2.04676863 2.3248782
0203_YH12_H_a100MCF7_r1.CEL 3.76300882 2.21061059 0.8928782
0203_YH15_H_a100MCF7_r2.CEL 3.48743637 1.85174042 0.7333814
0203_YH16_H_a100MCF7_r3.CEL 3.96519092 2.75890773 2.5180729
0203_YH11_H_MCF10A_r1.CEL 0.18696040 -0.16996777 -0.2838754
0203_YH26_H_MCF10A_r2.CEL 0.21779070 -0.08717746 -0.1663706
0203_YH27_H_MCF10A_r3.CEL 0.22559915 -0.13136386 -0.2611161
0403_YH38_H_a1MCF10A_r1.CEL 3.48817247 2.30788736 1.7173585
0403_YH39_H_a1MCF10A_r2_2.CEL 4.15783911 2.88076004 2.2823555
0403_YH40_H_a1MCF10A_r3.CEL 4.70124981 5.51637649 2.9428243
0203_YH21_H_a10MCF10A_r1.CEL 4.23862421 3.46260644 2.9303641
0203_YH22_H_a10MCF10A_r2.CEL 4.09426036 4.33692886 2.8721059
0203_YH23_H_a10MCF10A_r3_rescan.CEL 3.01584089 2.36558682 2.0238982
0403_YH34_H_a10MCF10A_r4.CEL 4.84782482 4.35551207 3.4385822
0203_YH13_H_a100MCF10A_r1.CEL 3.67658050 2.25769912 0.9946913
0203_YH17_H_a100MCF10A_r2.CEL 4.05732964 2.80248848 1.0429010
0203_YH18_H_a100MCF10A_r3.CEL 4.12729559 2.87986443 1.1631590
gapdh3/gapdhM
0203_YH10_H_MCF7_r1.CEL -0.17562350
0203_YH24_H_MCF7_r2.CEL -0.15533777
0203_YH25_H_MCF7_r3.CEL -0.18249084
0403_YH35_H_a1MCF7_r1_2.CEL 1.72047018
0403_YH36_H_a1MCF7_r2.CEL 2.30125117
0403_YH37_H_a1MCF7_r3_2.CEL 1.86583180
0203_YH14_H_a10MCF7_r1.CEL 0.66075371
0203_YH19_H_a10MCF7_r2.CEL 0.47114573
0203_YH20_H_a10MCF7_r3.CEL 0.96390226
0203_YH12_H_a100MCF7_r1.CEL 0.22147838
0203_YH15_H_a100MCF7_r2.CEL 0.26571755
0203_YH16_H_a100MCF7_r3.CEL 1.14600403
0203_YH11_H_MCF10A_r1.CEL -0.22330695
0203_YH26_H_MCF10A_r2.CEL -0.07151413
0203_YH27_H_MCF10A_r3.CEL -0.03365828
0403_YH38_H_a1MCF10A_r1.CEL 0.64065591
0403_YH39_H_a1MCF10A_r2_2.CEL 0.95401893
0403_YH40_H_a1MCF10A_r3.CEL 1.68738706
0203_YH21_H_a10MCF10A_r1.CEL 1.44442613
0203_YH22_H_a10MCF10A_r2.CEL 3.30882226
0203_YH23_H_a10MCF10A_r3_rescan.CEL 1.00908926
0403_YH34_H_a10MCF10A_r4.CEL 2.21949669
0203_YH13_H_a100MCF10A_r1.CEL 0.41270490
0203_YH17_H_a100MCF10A_r2.CEL 0.30771504
0203_YH18_H_a100MCF10A_r3.CEL 0.53894713
> avbg(qcs)
0203_YH10_H_MCF7_r1.CEL 0203_YH24_H_MCF7_r2.CEL
54.79781 56.55383
0203_YH25_H_MCF7_r3.CEL 0403_YH35_H_a1MCF7_r1_2.CEL
59.26790 59.52758
0403_YH36_H_a1MCF7_r2.CEL 0403_YH37_H_a1MCF7_r3_2.CEL
81.64647 93.72851
0203_YH14_H_a10MCF7_r1.CEL 0203_YH19_H_a10MCF7_r2.CEL
77.48265 76.41997
0203_YH20_H_a10MCF7_r3.CEL 0203_YH12_H_a100MCF7_r1.CEL
75.32842 82.97151
0203_YH15_H_a100MCF7_r2.CEL 0203_YH16_H_a100MCF7_r3.CEL
80.14180 82.91695
0203_YH11_H_MCF10A_r1.CEL 0203_YH26_H_MCF10A_r2.CEL
63.33604 59.67562
0203_YH27_H_MCF10A_r3.CEL 0403_YH38_H_a1MCF10A_r1.CEL
63.08459 81.97728
0403_YH39_H_a1MCF10A_r2_2.CEL 0403_YH40_H_a1MCF10A_r3.CEL
78.91661 68.31636
0203_YH21_H_a10MCF10A_r1.CEL 0203_YH22_H_a10MCF10A_r2.CEL
64.83461 61.27757
0203_YH23_H_a10MCF10A_r3_rescan.CEL 0403_YH34_H_a10MCF10A_r4.CEL
116.11718 92.70396
0203_YH13_H_a100MCF10A_r1.CEL 0203_YH17_H_a100MCF10A_r2.CEL
82.39357 80.43839
0203_YH18_H_a100MCF10A_r3.CEL
72.82438
> maxbg(qcs)
0203_YH10_H_MCF7_r1.CEL 0203_YH24_H_MCF7_r2.CEL
56.89239 59.84686
0203_YH25_H_MCF7_r3.CEL 0403_YH35_H_a1MCF7_r1_2.CEL
64.49775 62.54194
0403_YH36_H_a1MCF7_r2.CEL 0403_YH37_H_a1MCF7_r3_2.CEL
87.70483 103.33655
0203_YH14_H_a10MCF7_r1.CEL 0203_YH19_H_a10MCF7_r2.CEL
80.52142 81.11707
0203_YH20_H_a10MCF7_r3.CEL 0203_YH12_H_a100MCF7_r1.CEL
78.84589 89.24477
0203_YH15_H_a100MCF7_r2.CEL 0203_YH16_H_a100MCF7_r3.CEL
86.83688 97.07952
0203_YH11_H_MCF10A_r1.CEL 0203_YH26_H_MCF10A_r2.CEL
68.30370 62.90242
0203_YH27_H_MCF10A_r3.CEL 0403_YH38_H_a1MCF10A_r1.CEL
67.32432 90.65008
0403_YH39_H_a1MCF10A_r2_2.CEL 0403_YH40_H_a1MCF10A_r3.CEL
87.51111 79.99243
0203_YH21_H_a10MCF10A_r1.CEL 0203_YH22_H_a10MCF10A_r2.CEL
67.90225 64.38952
0203_YH23_H_a10MCF10A_r3_rescan.CEL 0403_YH34_H_a10MCF10A_r4.CEL
135.87939 100.41562
0203_YH13_H_a100MCF10A_r1.CEL 0203_YH17_H_a100MCF10A_r2.CEL
87.14364 86.77520
0203_YH18_H_a100MCF10A_r3.CEL
76.66844
> minbg(qcs)
0203_YH10_H_MCF7_r1.CEL 0203_YH24_H_MCF7_r2.CEL
51.95272 53.21018
0203_YH25_H_MCF7_r3.CEL 0403_YH35_H_a1MCF7_r1_2.CEL
54.04524 55.82989
0403_YH36_H_a1MCF7_r2.CEL 0403_YH37_H_a1MCF7_r3_2.CEL
75.88498 84.54410
0203_YH14_H_a10MCF7_r1.CEL 0203_YH19_H_a10MCF7_r2.CEL
71.73734 70.98562
0203_YH20_H_a10MCF7_r3.CEL 0203_YH12_H_a100MCF7_r1.CEL
71.13893 75.62456
0203_YH15_H_a100MCF7_r2.CEL 0203_YH16_H_a100MCF7_r3.CEL
74.40889 70.72456
0203_YH11_H_MCF10A_r1.CEL 0203_YH26_H_MCF10A_r2.CEL
58.56850 56.92324
0203_YH27_H_MCF10A_r3.CEL 0403_YH38_H_a1MCF10A_r1.CEL
58.85309 76.71987
0403_YH39_H_a1MCF10A_r2_2.CEL 0403_YH40_H_a1MCF10A_r3.CEL
70.66397 61.93977
0203_YH21_H_a10MCF10A_r1.CEL 0203_YH22_H_a10MCF10A_r2.CEL
61.17076 58.02036
0203_YH23_H_a10MCF10A_r3_rescan.CEL 0403_YH34_H_a10MCF10A_r4.CEL
95.00355 85.59183
0203_YH13_H_a100MCF10A_r1.CEL 0203_YH17_H_a100MCF10A_r2.CEL
77.05848 70.90370
0203_YH18_H_a100MCF10A_r3.CEL
69.39079
> spikeInProbes(qcs)
AFFX-r2-Ec-bioB-3_at AFFX-r2-Ec-bioC-3_at
0203_YH10_H_MCF7_r1.CEL 6.445937 7.798778
0203_YH24_H_MCF7_r2.CEL 6.503431 7.925939
0203_YH25_H_MCF7_r3.CEL 6.393249 7.788554
0403_YH35_H_a1MCF7_r1_2.CEL 11.436952 12.088198
0403_YH36_H_a1MCF7_r2.CEL 10.858187 11.415650
0403_YH37_H_a1MCF7_r3_2.CEL 10.390181 11.218265
0203_YH14_H_a10MCF7_r1.CEL 6.596963 8.278294
0203_YH19_H_a10MCF7_r2.CEL 6.903289 8.359344
0203_YH20_H_a10MCF7_r3.CEL 7.339286 8.786803
0203_YH12_H_a100MCF7_r1.CEL 5.993630 7.685893
0203_YH15_H_a100MCF7_r2.CEL 6.290555 7.826021
0203_YH16_H_a100MCF7_r3.CEL 6.740594 8.031900
0203_YH11_H_MCF10A_r1.CEL 6.426874 8.211754
0203_YH26_H_MCF10A_r2.CEL 6.731730 8.202263
0203_YH27_H_MCF10A_r3.CEL 6.374212 8.075213
0403_YH38_H_a1MCF10A_r1.CEL 9.251080 10.356051
0403_YH39_H_a1MCF10A_r2_2.CEL 10.266045 11.171241
0403_YH40_H_a1MCF10A_r3.CEL 11.271604 12.418644
0203_YH21_H_a10MCF10A_r1.CEL 8.394926 9.658082
0203_YH22_H_a10MCF10A_r2.CEL 9.537714 10.804072
0203_YH23_H_a10MCF10A_r3_rescan.CEL 6.599735 8.213599
0403_YH34_H_a10MCF10A_r4.CEL 8.882467 10.101293
0203_YH13_H_a100MCF10A_r1.CEL 6.802156 8.016934
0203_YH17_H_a100MCF10A_r2.CEL 6.530855 8.041842
0203_YH18_H_a100MCF10A_r3.CEL 6.504221 8.084243
AFFX-r2-Ec-bioD-3_at AFFX-r2-P1-cre-3_at
0203_YH10_H_MCF7_r1.CEL 9.503479 11.47752
0203_YH24_H_MCF7_r2.CEL 9.544291 11.51847
0203_YH25_H_MCF7_r3.CEL 9.495904 11.64499
0403_YH35_H_a1MCF7_r1_2.CEL 13.807572 15.48405
0403_YH36_H_a1MCF7_r2.CEL 13.299099 15.48526
0403_YH37_H_a1MCF7_r3_2.CEL 12.753151 14.54631
0203_YH14_H_a10MCF7_r1.CEL 9.906507 11.96170
0203_YH19_H_a10MCF7_r2.CEL 9.825725 12.11740
0203_YH20_H_a10MCF7_r3.CEL 10.316202 12.51155
0203_YH12_H_a100MCF7_r1.CEL 9.376227 11.73944
0203_YH15_H_a100MCF7_r2.CEL 9.388959 11.35048
0203_YH16_H_a100MCF7_r3.CEL 9.585132 11.78639
0203_YH11_H_MCF10A_r1.CEL 9.813676 11.99208
0203_YH26_H_MCF10A_r2.CEL 9.954069 12.03169
0203_YH27_H_MCF10A_r3.CEL 9.723605 11.79085
0403_YH38_H_a1MCF10A_r1.CEL 11.998551 14.00055
0403_YH39_H_a1MCF10A_r2_2.CEL 12.845073 14.60612
0403_YH40_H_a1MCF10A_r3.CEL 13.799019 15.90715
0203_YH21_H_a10MCF10A_r1.CEL 11.254889 13.39141
0203_YH22_H_a10MCF10A_r2.CEL 12.282388 14.39583
0203_YH23_H_a10MCF10A_r3_rescan.CEL 10.186251 12.69106
0403_YH34_H_a10MCF10A_r4.CEL 11.622218 13.84674
0203_YH13_H_a100MCF10A_r1.CEL 9.764205 12.02634
0203_YH17_H_a100MCF10A_r2.CEL 9.653164 12.05786
0203_YH18_H_a100MCF10A_r3.CEL 9.762951 11.98665
> qcProbes(qcs)
AFFX-HSAC07/X00351_3_at
0203_YH10_H_MCF7_r1.CEL 11.550089
0203_YH24_H_MCF7_r2.CEL 11.709283
0203_YH25_H_MCF7_r3.CEL 11.667964
0403_YH35_H_a1MCF7_r1_2.CEL 11.956522
0403_YH36_H_a1MCF7_r2.CEL 11.477514
0403_YH37_H_a1MCF7_r3_2.CEL 11.504157
0203_YH14_H_a10MCF7_r1.CEL 10.374330
0203_YH19_H_a10MCF7_r2.CEL 9.976329
0203_YH20_H_a10MCF7_r3.CEL 10.082873
0203_YH12_H_a100MCF7_r1.CEL 11.180869
0203_YH15_H_a100MCF7_r2.CEL 10.889904
0203_YH16_H_a100MCF7_r3.CEL 10.130475
0203_YH11_H_MCF10A_r1.CEL 11.023758
0203_YH26_H_MCF10A_r2.CEL 11.102372
0203_YH27_H_MCF10A_r3.CEL 11.006690
0403_YH38_H_a1MCF10A_r1.CEL 9.628146
0403_YH39_H_a1MCF10A_r2_2.CEL 10.123741
0403_YH40_H_a1MCF10A_r3.CEL 10.246260
0203_YH21_H_a10MCF10A_r1.CEL 9.425474
0203_YH22_H_a10MCF10A_r2.CEL 9.645739
0203_YH23_H_a10MCF10A_r3_rescan.CEL 8.907570
0403_YH34_H_a10MCF10A_r4.CEL 10.096445
0203_YH13_H_a100MCF10A_r1.CEL 10.010009
0203_YH17_H_a100MCF10A_r2.CEL 9.757457
0203_YH18_H_a100MCF10A_r3.CEL 9.757299
AFFX-HSAC07/X00351_5_at
0203_YH10_H_MCF7_r1.CEL 11.464486
0203_YH24_H_MCF7_r2.CEL 11.632304
0203_YH25_H_MCF7_r3.CEL 11.599923
0403_YH35_H_a1MCF7_r1_2.CEL 5.965993
0403_YH36_H_a1MCF7_r2.CEL 5.665837
0403_YH37_H_a1MCF7_r3_2.CEL 5.648802
0203_YH14_H_a10MCF7_r1.CEL 7.583093
0203_YH19_H_a10MCF7_r2.CEL 7.160968
0203_YH20_H_a10MCF7_r3.CEL 6.684872
0203_YH12_H_a100MCF7_r1.CEL 7.417860
0203_YH15_H_a100MCF7_r2.CEL 7.402468
0203_YH16_H_a100MCF7_r3.CEL 6.165284
0203_YH11_H_MCF10A_r1.CEL 10.836798
0203_YH26_H_MCF10A_r2.CEL 10.884582
0203_YH27_H_MCF10A_r3.CEL 10.781091
0403_YH38_H_a1MCF10A_r1.CEL 6.139974
0403_YH39_H_a1MCF10A_r2_2.CEL 5.965902
0403_YH40_H_a1MCF10A_r3.CEL 5.545010
0203_YH21_H_a10MCF10A_r1.CEL 5.186850
0203_YH22_H_a10MCF10A_r2.CEL 5.551479
0203_YH23_H_a10MCF10A_r3_rescan.CEL 5.891729
0403_YH34_H_a10MCF10A_r4.CEL 5.248620
0203_YH13_H_a100MCF10A_r1.CEL 6.333429
0203_YH17_H_a100MCF10A_r2.CEL 5.700127
0203_YH18_H_a100MCF10A_r3.CEL 5.630003
AFFX-HSAC07/X00351_M_at
0203_YH10_H_MCF7_r1.CEL 11.689362
0203_YH24_H_MCF7_r2.CEL 11.900552
0203_YH25_H_MCF7_r3.CEL 11.901835
0403_YH35_H_a1MCF7_r1_2.CEL 7.623952
0403_YH36_H_a1MCF7_r2.CEL 6.551514
0403_YH37_H_a1MCF7_r3_2.CEL 7.713071
0203_YH14_H_a10MCF7_r1.CEL 8.790955
0203_YH19_H_a10MCF7_r2.CEL 8.662190
0203_YH20_H_a10MCF7_r3.CEL 8.036104
0203_YH12_H_a100MCF7_r1.CEL 8.970258
0203_YH15_H_a100MCF7_r2.CEL 9.038164
0203_YH16_H_a100MCF7_r3.CEL 7.371568
0203_YH11_H_MCF10A_r1.CEL 11.193726
0203_YH26_H_MCF10A_r2.CEL 11.189550
0203_YH27_H_MCF10A_r3.CEL 11.138054
0403_YH38_H_a1MCF10A_r1.CEL 7.320259
0403_YH39_H_a1MCF10A_r2_2.CEL 7.242981
0403_YH40_H_a1MCF10A_r3.CEL 4.729883
0203_YH21_H_a10MCF10A_r1.CEL 5.962868
0203_YH22_H_a10MCF10A_r2.CEL 5.308810
0203_YH23_H_a10MCF10A_r3_rescan.CEL 6.541983
0403_YH34_H_a10MCF10A_r4.CEL 5.740933
0203_YH13_H_a100MCF10A_r1.CEL 7.752310
0203_YH17_H_a100MCF10A_r2.CEL 6.954969
0203_YH18_H_a100MCF10A_r3.CEL 6.877434
AFFX-HUMGAPDH/M33197_3_at
0203_YH10_H_MCF7_r1.CEL 11.38699
0203_YH24_H_MCF7_r2.CEL 11.52859
0203_YH25_H_MCF7_r3.CEL 11.57189
0403_YH35_H_a1MCF7_r1_2.CEL 11.86243
0403_YH36_H_a1MCF7_r2.CEL 11.43046
0403_YH37_H_a1MCF7_r3_2.CEL 12.23563
0203_YH14_H_a10MCF7_r1.CEL 11.37390
0203_YH19_H_a10MCF7_r2.CEL 11.73710
0203_YH20_H_a10MCF7_r3.CEL 11.89185
0203_YH12_H_a100MCF7_r1.CEL 11.45601
0203_YH15_H_a100MCF7_r2.CEL 11.22248
0203_YH16_H_a100MCF7_r3.CEL 11.54056
0203_YH11_H_MCF10A_r1.CEL 11.74507
0203_YH26_H_MCF10A_r2.CEL 12.09724
0203_YH27_H_MCF10A_r3.CEL 11.82442
0403_YH38_H_a1MCF10A_r1.CEL 12.50240
0403_YH39_H_a1MCF10A_r2_2.CEL 12.81315
0403_YH40_H_a1MCF10A_r3.CEL 11.88365
0203_YH21_H_a10MCF10A_r1.CEL 12.26114
0203_YH22_H_a10MCF10A_r2.CEL 11.77493
0203_YH23_H_a10MCF10A_r3_rescan.CEL 12.33582
0403_YH34_H_a10MCF10A_r4.CEL 11.92239
0203_YH13_H_a100MCF10A_r1.CEL 11.84918
0203_YH17_H_a100MCF10A_r2.CEL 11.61860
0203_YH18_H_a100MCF10A_r3.CEL 11.80744
AFFX-HUMGAPDH/M33197_5_at
0203_YH10_H_MCF7_r1.CEL 11.675220
0203_YH24_H_MCF7_r2.CEL 11.810917
0203_YH25_H_MCF7_r3.CEL 11.785602
0403_YH35_H_a1MCF7_r1_2.CEL 8.214196
0403_YH36_H_a1MCF7_r2.CEL 7.679575
0403_YH37_H_a1MCF7_r3_2.CEL 8.311971
0203_YH14_H_a10MCF7_r1.CEL 9.914406
0203_YH19_H_a10MCF7_r2.CEL 10.156923
0203_YH20_H_a10MCF7_r3.CEL 9.566967
0203_YH12_H_a100MCF7_r1.CEL 10.563134
0203_YH15_H_a100MCF7_r2.CEL 10.489099
0203_YH16_H_a100MCF7_r3.CEL 9.022490
0203_YH11_H_MCF10A_r1.CEL 12.028944
0203_YH26_H_MCF10A_r2.CEL 12.263607
0203_YH27_H_MCF10A_r3.CEL 12.085535
0403_YH38_H_a1MCF10A_r1.CEL 10.785040
0403_YH39_H_a1MCF10A_r2_2.CEL 10.530790
0403_YH40_H_a1MCF10A_r3.CEL 8.940830
0203_YH21_H_a10MCF10A_r1.CEL 9.330781
0203_YH22_H_a10MCF10A_r2.CEL 8.902825
0203_YH23_H_a10MCF10A_r3_rescan.CEL 10.311917
0403_YH34_H_a10MCF10A_r4.CEL 8.483813
0203_YH13_H_a100MCF10A_r1.CEL 10.854485
0203_YH17_H_a100MCF10A_r2.CEL 10.575697
0203_YH18_H_a100MCF10A_r3.CEL 10.644276
AFFX-HUMGAPDH/M33197_M_at
0203_YH10_H_MCF7_r1.CEL 11.562610
0203_YH24_H_MCF7_r2.CEL 11.683929
0203_YH25_H_MCF7_r3.CEL 11.754386
0403_YH35_H_a1MCF7_r1_2.CEL 10.141964
0403_YH36_H_a1MCF7_r2.CEL 9.129213
0403_YH37_H_a1MCF7_r3_2.CEL 10.369796
0203_YH14_H_a10MCF7_r1.CEL 10.713144
0203_YH19_H_a10MCF7_r2.CEL 11.265951
0203_YH20_H_a10MCF7_r3.CEL 10.927943
0203_YH12_H_a100MCF7_r1.CEL 11.234534
0203_YH15_H_a100MCF7_r2.CEL 10.956762
0203_YH16_H_a100MCF7_r3.CEL 10.394559
0203_YH11_H_MCF10A_r1.CEL 11.968376
0203_YH26_H_MCF10A_r2.CEL 12.168751
0203_YH27_H_MCF10A_r3.CEL 11.858077
0403_YH38_H_a1MCF10A_r1.CEL 11.861742
0403_YH39_H_a1MCF10A_r2_2.CEL 11.859127
0403_YH40_H_a1MCF10A_r3.CEL 10.196267
0203_YH21_H_a10MCF10A_r1.CEL 10.816719
0203_YH22_H_a10MCF10A_r2.CEL 8.466108
0203_YH23_H_a10MCF10A_r3_rescan.CEL 11.326726
0403_YH34_H_a10MCF10A_r4.CEL 9.702898
0203_YH13_H_a100MCF10A_r1.CEL 11.436472
0203_YH17_H_a100MCF10A_r2.CEL 11.310883
0203_YH18_H_a100MCF10A_r3.CEL 11.268488
> percent.present(qcs)
0203_YH10_H_MCF7_r1.CEL.present
57.24543
0203_YH24_H_MCF7_r2.CEL.present
56.10106
0203_YH25_H_MCF7_r3.CEL.present
55.37405
0403_YH35_H_a1MCF7_r1_2.CEL.present
32.76938
0403_YH36_H_a1MCF7_r2.CEL.present
31.13136
0403_YH37_H_a1MCF7_r3_2.CEL.present
35.28699
0203_YH14_H_a10MCF7_r1.CEL.present
48.12189
0203_YH19_H_a10MCF7_r2.CEL.present
48.64695
0203_YH20_H_a10MCF7_r3.CEL.present
48.58861
0203_YH12_H_a100MCF7_r1.CEL.present
50.53628
0203_YH15_H_a100MCF7_r2.CEL.present
52.21469
0203_YH16_H_a100MCF7_r3.CEL.present
49.03738
0203_YH11_H_MCF10A_r1.CEL.present
53.22892
0203_YH26_H_MCF10A_r2.CEL.present
51.65373
0203_YH27_H_MCF10A_r3.CEL.present
52.91029
0403_YH38_H_a1MCF10A_r1.CEL.present
41.40825
0403_YH39_H_a1MCF10A_r2_2.CEL.present
33.62653
0403_YH40_H_a1MCF10A_r3.CEL.present
27.55913
0203_YH21_H_a10MCF10A_r1.CEL.present
41.87048
0203_YH22_H_a10MCF10A_r2.CEL.present
33.24059
0203_YH23_H_a10MCF10A_r3_rescan.CEL.present
40.26837
0403_YH34_H_a10MCF10A_r4.CEL.present
39.77920
0203_YH13_H_a100MCF10A_r1.CEL.present
47.58785
0203_YH17_H_a100MCF10A_r2.CEL.present
48.04560
0203_YH18_H_a100MCF10A_r3.CEL.present
48.35076
> plot(qcs)
> sfs(qcs)
[1] 0.2916603 0.3477972 0.3185392 3.5923019 3.1613079 2.0133039 0.3854621
[8] 0.4132180 0.4827030 0.2875890 0.2849745 0.3764849 0.4202530 0.5789222
[15] 0.3948337 0.9238817 2.2926538 4.0247478 0.9453697 1.9614400 0.8415359
[22] 1.0680470 0.4512004 0.3740874 0.4872075
> target(qcs)
[1] 100
> ratios(qcs)
actin3/actin5 actin3/actinM gapdh3/gapdh5
0203_YH10_H_MCF7_r1.CEL 0.08560278 -0.13927277 -0.2882327
0203_YH24_H_MCF7_r2.CEL 0.07697926 -0.19126947 -0.2823266
0203_YH25_H_MCF7_r3.CEL 0.06804130 -0.23387107 -0.2137072
0403_YH35_H_a1MCF7_r1_2.CEL 5.99052862 4.33256971 3.6482383
0403_YH36_H_a1MCF7_r2.CEL 5.81167692 4.92600016 3.7508887
0403_YH37_H_a1MCF7_r3_2.CEL 5.85535460 3.79108521 3.9236571
0203_YH14_H_a10MCF7_r1.CEL 2.79123667 1.58337477 1.4594917
0203_YH19_H_a10MCF7_r2.CEL 2.81536065 1.31413895 1.5801740
0203_YH20_H_a10MCF7_r3.CEL 3.39800077 2.04676863 2.3248782
0203_YH12_H_a100MCF7_r1.CEL 3.76300882 2.21061059 0.8928782
0203_YH15_H_a100MCF7_r2.CEL 3.48743637 1.85174042 0.7333814
0203_YH16_H_a100MCF7_r3.CEL 3.96519092 2.75890773 2.5180729
0203_YH11_H_MCF10A_r1.CEL 0.18696040 -0.16996777 -0.2838754
0203_YH26_H_MCF10A_r2.CEL 0.21779070 -0.08717746 -0.1663706
0203_YH27_H_MCF10A_r3.CEL 0.22559915 -0.13136386 -0.2611161
0403_YH38_H_a1MCF10A_r1.CEL 3.48817247 2.30788736 1.7173585
0403_YH39_H_a1MCF10A_r2_2.CEL 4.15783911 2.88076004 2.2823555
0403_YH40_H_a1MCF10A_r3.CEL 4.70124981 5.51637649 2.9428243
0203_YH21_H_a10MCF10A_r1.CEL 4.23862421 3.46260644 2.9303641
0203_YH22_H_a10MCF10A_r2.CEL 4.09426036 4.33692886 2.8721059
0203_YH23_H_a10MCF10A_r3_rescan.CEL 3.01584089 2.36558682 2.0238982
0403_YH34_H_a10MCF10A_r4.CEL 4.84782482 4.35551207 3.4385822
0203_YH13_H_a100MCF10A_r1.CEL 3.67658050 2.25769912 0.9946913
0203_YH17_H_a100MCF10A_r2.CEL 4.05732964 2.80248848 1.0429010
0203_YH18_H_a100MCF10A_r3.CEL 4.12729559 2.87986443 1.1631590
gapdh3/gapdhM
0203_YH10_H_MCF7_r1.CEL -0.17562350
0203_YH24_H_MCF7_r2.CEL -0.15533777
0203_YH25_H_MCF7_r3.CEL -0.18249084
0403_YH35_H_a1MCF7_r1_2.CEL 1.72047018
0403_YH36_H_a1MCF7_r2.CEL 2.30125117
0403_YH37_H_a1MCF7_r3_2.CEL 1.86583180
0203_YH14_H_a10MCF7_r1.CEL 0.66075371
0203_YH19_H_a10MCF7_r2.CEL 0.47114573
0203_YH20_H_a10MCF7_r3.CEL 0.96390226
0203_YH12_H_a100MCF7_r1.CEL 0.22147838
0203_YH15_H_a100MCF7_r2.CEL 0.26571755
0203_YH16_H_a100MCF7_r3.CEL 1.14600403
0203_YH11_H_MCF10A_r1.CEL -0.22330695
0203_YH26_H_MCF10A_r2.CEL
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and