Question: Including technical and biological replicates in Limma block analysis?
3
gravatar for vas
5.0 years ago by
vas40
Chicago
vas40 wrote:

Hi I have a question regarding the Limma code.

I have control samples (6 biological replicates, and each of the inturn have a technical replicate), I need to include all of them (12 samples) in contrast analysis.

Targets file:

Sample        Block        Treatment

Control11        1             Control
Control12        2             Control
Control13        3             Control
Control14        4             Control
Control15        5             Control
Control16        6             Control
Control21        1             Control
Control22        2             Control
Control23        3             Control
Control24        4             Control
Control25        5             Control
Control26        6             Control
Treat1             1             treatment
Treat2             2             treatment
Treat3             3             treatment
Treat4             4             treatment
Treat5             5             treatment
Treat6             6             treatment

In  the targets file, Control11 and control21 and technical replicates and so on.

So, I need  to compare 12  control samples (6*2) with 6 treatment samples.

I am performing block analysis (paired samples) to account for interindividual variation.

Please let  me know the best way to perform this Limma block (paired) analysis.

Thanks a lot in advance

Here is my code:

targets <-readTargets()
treat <-factor(targets$treatment)
block<- factor(targets$block)
ct <- factor(targets$treatment)
design <- model.matrix(~0+ct)
colnames(design) <- levels(ct)
dupcor <- duplicateCorrelation(maqc.norm.filt,design,block=targets$block)
fit <- lmFit(maqc.norm.filt,design,block=targets$block,correlation=dupcor$consensus.correlation)
contrasts <- makeContrasts(treatment-control, levels=design)
contr.fit <- eBayes(contrasts.fit(fit,contrasts))
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by vas40

(Repeated Targets file as given above)

ADD REPLYlink modified 5.0 years ago by Gordon Smyth39k • written 5.0 years ago by vas40
Answer: Including technical and biological replicates in Limma block analysis?
1
gravatar for Aaron Lun
5.0 years ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

No, your code is not ideal. You are treating technical replicates and pairing as equivalent whereas they are somewhat different things.

The limma User's Guide explains (Section 9.4.1) that paired designs are analyzed by including the pairing factor (Subject) in the design matrix.

For your experiment there is nothing to be gained by keeping the technical replicates separate. You may as well average them and do a standard paired analysis. This isn't hard:

y <- new("EList",list(E=maqc.norm.filt,targets=targets))
Sample <- paste(targets$Treatment,targets$Block,sep=".")
y2 <- avearrays(y, ID=Sample)
treat <- factor(y2$targets$Treatment)
pair <- factor(y2$targets$Block)
design <- model.matrix(~treat+pair)
fit <- eBayes(lmFit(y2, design))
topTable(fit,coef=2)

ADD COMMENTlink modified 5.0 years ago by Gordon Smyth39k • written 5.0 years ago by Aaron Lun25k

Dear Gordon,

I am facing the following error.

y2 <- avearrays(y, ID=Sample)

Error: argument "i" is missing, with no default

Please help me to solve this error.

Thanks in advance

ADD REPLYlink written 5.0 years ago by vas40

What does traceback() say when you run it immediately after the error? I assume you're using the latest version of Bioconductor and limma.

ADD REPLYlink written 5.0 years ago by Aaron Lun25k

Dear Aaron,

This is the output from traceback()

5: subsetListOfArrays(object, i, j, IJ = IJ, IX = IX, I = I, JX = JX)
4: `[.EList`(x, , !d)
3: x[, !d]
2: avearrays.EList(y, ID = Sample)
1: avearrays(y, ID = Sample)

ADD REPLYlink written 5.0 years ago by vas40

Dear Aaron.

This is the output from sessionInfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] splines   parallel  stats4    stats     graphics  grDevices
 [7] utils     datasets  methods   base     

other attached packages:
 [1] statmod_1.4.20            illuminaHumanv4.db_1.24.0
 [3] org.Hs.eg.db_3.0.0        RSQLite_1.0.0            
 [5] DBI_0.3.1                 AnnotationDbi_1.28.1     
 [7] GenomeInfoDb_1.2.3        IRanges_2.0.0            
 [9] S4Vectors_0.4.0           Biobase_2.26.0           
[11] BiocGenerics_0.12.1       limma_3.22.1             

loaded via a namespace (and not attached):
[1] tools_3.1.1

ADD REPLYlink written 5.0 years ago by vas40

Hmm... What is maqc.norm.filt? It should be a numeric matrix with number of columns equal to the number of rows in target. Perhaps you could also show the output of:

print(y)
print(Sample)
ADD REPLYlink written 5.0 years ago by Aaron Lun25k

Suri, please keep things on-list (i.e., on the support site); you'll get more/better help that way. Anyway, looking at the script you sent me, maqc.norm.filt seems to be an EList object. This will generate the observed error during subsetting. To get around this, you just need to define:

y <- maqc.norm.filt
y$targets <- targets

There's no need to construct a new EList object, because maqc.norm.filt is already one.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Aaron Lun25k

Hi Aaron,

I tried to create the EList as you mentioned with the command  y <-maqc.norm.filt

But It seems treat and pair factors carrying no information from the target file.

I dont know if I should create the new Elist object with the following command to have the target information

y <- new("EList",list(E=maqc.norm.filt,targets=targets))

 

targets <-readTargets()
y <-maqc.norm.filt
Sample <- paste(targets$Treatment,targets$Block,sep=".")
y2<- avearrays(y, ID=Sample)
treat <- factor(y2$targets$Treatment)
pair <- factor(y2$targets$Block)
design <- model.matrix(~treat+pair)

Error: Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels

treat and pair  both are factors  with 0 levels.

ADD REPLYlink written 5.0 years ago by vas40

> print(y)

An object of class "EList"
$source
[1] "illumina"

$E
          DMSO_H1   DMSO_H3   DMSO_H2   DMSO_H4   DMSO_H6   DMSO_H5  CH1.5_H1
6450255  4.903814  4.709843  4.605154  4.349392  4.627624  4.747999  4.525305
6370619  4.787750  4.658187  6.334636  6.976980  4.537049  4.834669  4.513528
2600039  9.734036  9.879677 10.141838  9.972583  8.891848 10.075864 10.297946
2650615 10.331254 10.727561 10.844507 10.866681 10.116807 10.663791 10.665097
5340672  5.490635  6.442971  6.273935  6.152497  5.522529  6.304948  4.926749
         CH1.5_H2   EE75_H3   EE75_H1  EE75_H2   EE75_H6   EE75_H4   EE75_H5
6450255  4.527058  4.718276  4.765861 4.501529  4.602818  4.494968  4.470732
6370619  4.728638  4.635120  4.523159 4.646561  4.483844  5.302645  4.720783
2600039 10.128726 10.394483  9.770742 9.336360  9.206441  9.059156  9.929407
2650615 10.752102 10.723947 10.515010 9.837166 10.415661 10.217529 10.773916
5340672  5.259134  5.977356  4.823451 4.543041  5.606076  6.068607  6.203764
           CH1_H3    CH1_H1    CH1_H2    CH1_H4    CH1_H6    CH1_H5   ND4_H2
6450255  4.671222  4.680834  4.449080  4.431277  4.957755  4.480258 4.679074
6370619  4.609719  4.510802  4.649475  5.041760  5.544203  4.852887 4.422638
2600039  9.525957  9.648000  9.964435  9.482758  9.373494 10.071145 8.523127
2650615 10.286467 10.253820 10.552588 10.421406 10.120820 10.876723 9.302150
5340672  5.168012  4.776770  5.186432  5.913991  4.688725  6.331758 4.818276
          ND4_H3   ND4_H1   ND4_H5   ND4_H6   ND4_H4    BZ5_H2    BZ5_H3   BZ5_H1
6450255 4.581165 4.668823 4.488177 4.700258 4.406585  4.617363  4.619910 4.657489
6370619 4.391702 4.555745 4.553796 4.502965 4.497709  5.962848  4.828866 4.493629
2600039 8.234401 7.694515 8.863548 8.002846 7.583209  9.794260  9.814602 9.359686
2650615 9.060281 8.647932 9.170649 8.577708 8.425709 10.408879 10.612341 9.850973
5340672 4.795569 4.742779 4.369387 4.974876 4.951860  6.004215  6.056134 5.294387
           BZ5_H5   BZ5_H6    BZ5_H4   MT75_H1   MT75_H3   MT75_H2   MT75_H4
6450255  4.330587 4.446776  4.504667  4.454645  4.463520  4.530728  4.512937
6370619  4.405141 4.484926  6.280663  4.645951  4.654933  5.021089  4.597270
2600039  9.652520 8.784064  9.762324  9.773332 10.199029 10.145594  9.578817
2650615 10.624952 9.800025 10.568740 10.661449 10.960095 10.893888 10.662634
5340672  5.480844 5.049366  6.034373  5.284335  5.700933  6.238301  5.690956
          MT75_H6   MT75_H5   EE50_H3   EE50_H1   EE50_H2   EE50_H6   EE50_H4
6450255  4.400109  4.671953  4.678587  4.617166  4.484790  4.601380  4.512076
6370619  4.603749  4.577261  4.554828  4.725901  4.981968  4.353923  5.775325
2600039  9.194918 10.143571 10.282851  9.436647  9.885358  9.325237  9.575840
2650615 10.289363 10.942139 11.070155 10.219427 10.494933 10.338880 10.556112
5340672  5.454203  6.393641  5.938923  5.715864  5.454912  5.689075  6.253117
          EE50_H5    CL5_H3   CL5_H2    CL5_H1    CL5_H6    CL5_H5   CL5_H4
6450255  4.504156  4.880783 4.614806  4.367977  4.619473  4.378908 4.498000
6370619  4.840762  4.623800 4.513008  4.798771  5.306580  4.736916 6.018030
2600039  9.721348  9.686676 9.216193 10.404439  9.833081 10.003485 8.642096
2650615 10.520175 10.354143 9.795854 11.007691 10.646550 10.712979 9.672202
5340672  5.922297  6.024463 4.478683  5.980539  6.392157  6.076667 5.105133
         BZ7.5_H2 BZ7.5_H1  BZ7.5_H3 BZ7.5_H5 BZ7.5_H4 BZ7.5_H6    CS9_H2    CS9_H3
6450255  4.890524 4.712761  4.479475 4.355023 4.476565 4.424028  4.640228  4.649825
6370619  5.659260 4.447984  4.551914 4.510025 4.951265 4.471194  6.539877  5.309285
2600039  9.620083 8.881990  9.305321 8.753834 8.331236 9.148807 10.698408  9.871459
2650615 10.251790 9.607584 10.009697 9.578134 9.316314 9.847721 11.135228 10.550282
5340672  5.453980 5.296496  5.652899 5.549381 5.385193 4.530852  6.521922  5.567815
           CS9_H1    CS9_H5    CS9_H6    CS9_H4   MT50_H3  MT50_H1   MT50_H2
6450255  4.491868  4.416724  4.618026  4.305740  4.684478 4.388660  4.406079
6370619  4.507075  4.550879  4.519359  5.851106  4.401294 4.285267  5.014389
2600039  9.700603 10.317298  9.280580  9.487540 10.023509 9.179268 10.109257
2650615 10.186085 10.898286 10.366019 10.413198 10.758953 9.804011 10.857777
5340672  5.712879  6.162490  5.904147  5.659743  5.699946 5.083214  6.153269
          MT50_H6   MT50_H4   MT50_H5   CS15_H3   CS15_H2   CS15_H1   CS15_H6
6450255  4.562796  4.531103  4.509116  4.712761  4.441653  4.572634  4.498708
6370619  4.486096  5.123386  4.538133  5.177698  5.819124  4.409133  4.677912
2600039  9.526660  9.493633  9.920629 10.276326 10.492627  9.914702  9.540717
2650615 10.439501 10.334598 10.940484 10.896866 11.051266 10.689008 10.434026
5340672  5.267695  6.329089  6.329393  6.678717  6.669730  5.583545  5.957483
          CS15_H5  CS15_H4  BZ2.5_H2  BZ2.5_H1  BZ2.5_H3  BZ2.5_H5  BZ2.5_H4
6450255  4.497684 4.349748  4.508864  4.594730  4.770575  4.398534  4.523300
6370619  4.813736 5.998756  6.371744  4.755435  5.208306  4.866639  6.499164
2600039 10.137245 8.916559  9.669009  9.666852  9.648000  9.401410  9.477082
2650615 10.970789 9.941456 10.667920 10.313996 10.649338 10.108342 10.584240
5340672  6.633213 5.811167  5.830900  5.521475  5.702875  4.994547  6.087828
         BZ2.5_H6   AN25_H1   AN25_H3   AN25_H2   AN25_H4  AN25_H6   AN25_H5
6450255  4.393818  4.468366  4.586119  4.507869  4.501786 4.340971  4.515018
6370619  4.513470  4.680244  4.591970  5.266079  6.021561 4.493474  5.001771
2600039  8.970824  9.443269 10.146628 10.166387  9.427241 8.897306  9.884435
2650615 10.046908 10.060991 10.796009 10.785191 10.554915 9.985992 10.684761
5340672  5.399400  5.701206  6.067831  6.335508  5.906265 5.379335  6.511833
            BA_H1     BA_H2     BA_H3     BA_H4     BA_H5    BA_H6    AP5_H3
6450255  4.632858  4.611027  4.699643  4.568932  4.518737 4.479249  4.660107
6370619  4.567016  6.505851  5.121019  6.332026  4.638917 4.598140  4.606465
2600039  9.307911  9.930318  9.763065  9.537033  9.566199 8.391456  9.307324
2650615 10.005490 10.613305 10.497469 10.561397 10.481133 9.620825 10.245766
5340672  5.229307  6.187494  6.197706  6.266282  5.857607 5.082182  4.755169
          AP5_H2    AP5_H1    AP5_H6    AP5_H5   AP5_H4   CS12_H2   CS12_H1
6450255 4.432189  4.680639  4.526429  4.358277 4.519151  4.419580  4.418647
6370619 4.472032  4.491598  4.983065  4.710959 4.899471  5.700707  4.722500
2600039 9.216193  9.815396  9.077840 10.318443 8.182337 10.477476  9.952592
2650615 9.804800 10.468842 10.374750 11.195689 9.025592 11.087920 10.661449
5340672 4.719730  4.689747  5.822611  5.489171 4.802831  6.399172  5.892255
          CS12_H3   CS12_H5  CS12_H4   CS12_H6   CP30_H2  CP30_H1   CP30_H3
6450255  4.494855  4.627601 4.423364  4.542219  4.580706 4.801414  4.450813
6370619  4.508023  4.807383 6.114490  5.090126  4.972981 4.720467  4.945365
2600039  9.959806 10.012395 9.194316  9.665162  9.516927 8.877275  9.732374
2650615 10.899839 10.801564 9.922466 10.639153 10.195203 9.359079 10.665097
5340672  6.237440  6.083876 5.384220  6.503469  5.428952 4.999045  5.859124
          CP30_H5  CP30_H4  CP30_H6  MT100_H1  MT100_H3  MT100_H2  MT100_H4
6450255  4.455713 4.434051 4.659258  4.482232  4.489141  4.867923  4.568000
6370619  4.693283 5.289819 4.695631  4.756971  4.461725  4.803240  6.286450
2600039  9.107683 8.931378 8.736340 10.121727  9.283240 10.138210  8.861384
2650615 10.106654 9.856841 9.873025 10.706317 10.341059 10.860744 10.421406
5340672  5.778799 5.782452 5.334644  5.502447  4.403550  5.993699  5.344300
         MT100_H6  MT100_H5   CP20_H2   CP20_H3  CP20_H1   CP20_H5  CP20_H6
6450255  4.469831  4.439700  4.627003  4.488811 4.669207  4.535702 4.383711
6370619  4.639208  4.540905  5.528773  4.575680 4.614759  4.858355 4.354927
2600039  9.330426 10.151813  9.754555  9.847721 8.563045 10.157700 8.890750
2650615 10.727561 11.063890 10.675639 10.608654 9.438651 10.963135 9.967191
5340672  5.509229  6.248400  6.107093  5.813901 4.776508  6.329974 5.721079
          CP20_H4  AN50_H1   AN50_H3   AN50_H2   AN50_H4   AN50_H6   AN50_H5
6450255  4.402309 4.899717  4.412499  4.401208  4.463530  4.463797  4.458104
6370619  5.580539 4.503561  4.369376  4.965367  4.847102  4.615695  4.680768
2600039  9.293465 9.203403  9.695266 10.257862  9.269168  9.304686  9.680357
2650615 10.411070 9.920629 10.544964 10.922064 10.072971 10.004519 10.516288
5340672  5.851410 5.458391  6.072569  6.467846  6.078779  5.554296  6.088114
        CL2.5_H3  CL2.5_H1 CL2.5_H2 CL2.5_H6 CL2.5_H4  CL2.5_H5   ND8_H2   ND8_H1
6450255 4.618704  4.450149 4.513470 4.449779 4.423343  4.562372 4.301109 4.454774
6370619 4.518066  4.772809 4.595474 4.719430 5.073731  4.578687 5.005877 4.554619
2600039 8.672534  9.795043 9.479969 8.967939 7.706122  9.578817 8.127147 7.567983
2650615 9.452675 10.210553 9.981566 9.979696 8.731316 10.147673 8.798286 8.195899
5340672 4.634278  4.991074 5.728544 5.609785 4.586749  4.809610 4.891443 4.506840
          ND8_H3   ND8_H5   ND8_H4   ND8_H6   CL1_H1   CL1_H2   CL1_H3   CL1_H4
6450255 4.629951 4.510308 4.490092 4.511770 4.760680 4.637602 4.444958 4.446987
6370619 4.488987 4.370763 4.671036 4.541335 4.624829 4.269178 4.327750 4.638628
2600039 8.273550 8.745264 7.187920 7.456064 8.757121 7.985396 8.337432 7.306707
2650615 9.164499 9.484770 8.127538 8.703938 9.391428 8.864076 9.231584 8.563045
5340672 4.909037 4.741112 4.796850 4.886008 4.848268 4.519034 5.138689 4.771241
          CL1_H5   CL1_H6   EE25_H3   EE25_H1   EE25_H2   EE25_H6   EE25_H4
6450255 4.441592 4.557038  4.498591  4.514451  4.455160  4.566775  4.629973
6370619 4.797927 4.413028  4.839151  4.632377  5.208306  4.602137  5.409806
2600039 8.611683 8.509196 10.390134  9.700603  9.970747  9.238444  9.994690
2650615 9.617960 9.361565 10.976932 10.103788 10.670412 10.311765 10.624952
5340672 4.885601 4.624023  6.237735  5.866238  6.205683  6.111242  6.036014
          EE25_H5  CH0.5_H3 CH0.5_H1 CH0.5_H2  CH0.5_H4  CH0.5_H5 CH0.5_H6  ND15_H3
6450255  4.447736  4.449719 4.741178 4.408685  4.789583  4.332952 4.458058 4.512666
6370619  4.782719  4.574814 4.538687 4.390515  5.745686  4.654205 4.371927 4.626390
2600039  9.656997 10.035249 8.975861 9.163303  9.212551 10.239517 8.892913 8.218945
2650615 10.793366 10.544964 9.822908 9.864511 10.404439 11.106206 9.857742 9.283240
5340672  6.236304  5.456783 5.213530 4.888778  5.933440  6.103643 5.154333 4.855808
         ND15_H2  ND15_H1  ND15_H6  ND15_H5  ND15_H4   AN75_H1   AN75_H2   AN75_H3
6450255 4.398984 4.678912 4.863836 4.618821 4.545098  4.383037  4.483048  4.690212
6370619 4.402136 4.569159 4.480130 4.387809 4.618290  4.469951  4.927168  4.375267
2600039 7.284664 7.469924 7.376441 7.598028 6.931530  9.359686  9.906145  9.993023
2650615 8.234401 8.145783 8.562489 8.163420 7.741113 10.197161 10.653463 10.698408
5340672 4.433339 4.635865 4.806134 4.733823 4.618180  5.173267  5.905710  5.936636
          AN75_H4   AN75_H5   AN75_H6 CH0.25_H3 CH0.25_H4 CH0.25_H6 CH0.25_H5
6450255  4.489500  4.424350  4.384942  4.514472  4.596128  4.547200  4.512796
6370619  5.118469  4.483187  4.682197  4.448356  4.479899  4.539798  4.497349
2600039  9.166186  9.803254  9.303458  8.456621  8.012486  8.826016  8.428008
2650615 10.113142 10.505490 10.185116  9.496313  8.786060  9.625928  9.179268
5340672  5.975510  6.299185  5.346726  4.619266  4.851420  5.243607  5.263124
        AP2.5_H2 AP2.5_H1  AP2.5_H3  AP2.5_H5 AP2.5_H4 AP2.5_H6    C24_H2    C24_H3
6450255 4.563230 4.513202  4.476125  4.328996 4.536373 4.589241  4.587678  4.430036
6370619 4.617351 4.494760  4.467841  4.631247 5.999022 4.402448  5.975510  5.219874
2600039 7.623937 9.390119  9.435340 10.566257 8.888484 9.197930 10.253820  9.902924
2650615 8.339226 9.965471 10.237695 11.167714 9.699825 9.774927 11.125019 10.618273
5340672 4.458151 4.514683  5.342928  6.165793 4.785086 5.818050  6.503469  5.838846
           C24_H1    C24_H5    C24_H6    C24_H4   CP10_H3   CP10_H2   CP10_H6
6450255  4.560794  4.384333  4.722985  4.634487  4.589903  4.314731  4.461025
6370619  4.766154  4.594888  4.319459  5.160191  4.589221  5.688428  4.411411
2600039  9.422557  9.926004  9.132540  9.227808  9.661593 10.056167  9.020507
2650615 10.010594 10.705107 10.284353 10.286467 10.690283 10.537405 10.119771
5340672  4.950381  5.499835  5.920484  6.102005  5.758106  6.056134  5.487394
          CP10_H5  CP40_H1  CP40_H4
6450255  4.390493 4.572498 4.526817
6370619  4.702240 4.467217 5.194662
2600039  9.709559 8.721728 8.707923
2650615 10.608654 9.478511 9.478511
5340672  5.911635 4.489191 5.237454
34471 more rows ...

$genes
[1] "7A5"  "A1BG" "A1CF" "A1CF" "A1CF"
34471 more rows ...

$other
$Detection Pval
            DMSO_H1     DMSO_H3     DMSO_H2     DMSO_H4     DMSO_H6     DMSO_H5
6450255 0.037662340 0.077922080 0.153246800 0.810389600 0.120779200 0.075324680
6370619 0.072727270 0.103896100 0.002597403 0.001298701 0.253246800 0.041558440
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.005194805 0.001298701 0.002597403 0.002597403 0.001298701 0.001298701
          CH1.5_H1    CH1.5_H2     EE75_H3    EE75_H1   EE75_H2     EE75_H6
6450255 0.31948050 0.314285700 0.089610390 0.06883117 0.3389610 0.176623400
6370619 0.33766230 0.067532460 0.157142900 0.30259740 0.1298701 0.387013000
2600039 0.00000000 0.000000000 0.000000000 0.00000000 0.0000000 0.000000000
2650615 0.00000000 0.000000000 0.000000000 0.00000000 0.0000000 0.000000000
5340672 0.05324675 0.006493506 0.001298701 0.06103896 0.2480519 0.001298701
            EE75_H4     EE75_H5     CH1_H3     CH1_H1      CH1_H2      CH1_H4
6450255 0.345454500 0.402597400 0.11948050 0.16103900 0.463636400 0.559740200
6370619 0.003896104 0.048051950 0.17142860 0.37402600 0.115584400 0.015584420
2600039 0.000000000 0.000000000 0.00000000 0.00000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.00000000 0.00000000 0.000000000 0.000000000
5340672 0.003896104 0.002597403 0.01038961 0.08831169 0.006493506 0.002597403
             CH1_H6      CH1_H5     ND4_H2     ND4_H3     ND4_H1    ND4_H5
6450255 0.036363640 0.364935100 0.09090909 0.19480520 0.10909090 0.3480519
6370619 0.007792208 0.019480520 0.54025970 0.66103890 0.23246750 0.2415584
2600039 0.000000000 0.000000000 0.00000000 0.00000000 0.00000000 0.0000000
2650615 0.000000000 0.000000000 0.00000000 0.00000000 0.00000000 0.0000000
5340672 0.122077900 0.002597403 0.03896104 0.03896104 0.07142857 0.7350649
            ND4_H6     ND4_H4      BZ5_H2      BZ5_H3      BZ5_H1      BZ5_H5
6450255 0.09870130 0.61818180 0.137662300 0.149350600 0.128571400 0.890909100
6370619 0.34805190 0.36623380 0.002597403 0.041558440 0.363636400 0.622077900
2600039 0.00000000 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.00000000 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.02077922 0.01038961 0.002597403 0.001298701 0.006493506 0.006493506
            BZ5_H6      BZ5_H4     MT75_H1     MT75_H3     MT75_H2     MT75_H4
6450255 0.47532470 0.341558500 0.477922100 0.463636400 0.274026000 0.353246700
6370619 0.35844160 0.001298701 0.142857100 0.129870100 0.010389610 0.200000000
2600039 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.01168831 0.002597403 0.003896104 0.002597403 0.001298701 0.003896104
            MT75_H6     MT75_H5     EE50_H3     EE50_H1     EE50_H2     EE50_H6
6450255 0.640259700 0.106493500 0.115584400 0.167532500 0.379220800 0.164935100
6370619 0.155844200 0.206493500 0.244155800 0.087012980 0.012987010 0.781818200
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.003896104 0.002597403 0.002597403 0.001298701 0.002597403 0.001298701
            EE50_H4     EE50_H5      CL5_H3    CL5_H2      CL5_H1      CL5_H6
6450255 0.280519500 0.355844200 0.058441560 0.1714286 0.787013000 0.206493500
6370619 0.003896104 0.046753250 0.222077900 0.3220779 0.097402590 0.016883120
2600039 0.000000000 0.000000000 0.000000000 0.0000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.0000000 0.000000000 0.000000000
5340672 0.002597403 0.002597403 0.002597403 0.4051948 0.005194805 0.002597403
             CL5_H5      CL5_H4    BZ7.5_H2    BZ7.5_H1    BZ7.5_H3    BZ7.5_H5
6450255 0.736363600 0.368831200 0.024675320 0.089610390 0.403896100 0.770129900
6370619 0.079220780 0.003896104 0.002597403 0.498701300 0.246753200 0.319480500
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.003896104 0.014285710 0.003896104 0.005194805 0.002597403 0.003896104
           BZ7.5_H4  BZ7.5_H6      CS9_H2      CS9_H3      CS9_H1      CS9_H5
6450255 0.379220800 0.6350650 0.151948000 0.141558400 0.433766200 0.605194800
6370619 0.012987010 0.4922078 0.001298701 0.005194805 0.390909100 0.248051900
2600039 0.000000000 0.0000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.0000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.006493506 0.3584416 0.001298701 0.003896104 0.002597403 0.002597403
             CS9_H6      CS9_H4     MT50_H3     MT50_H1     MT50_H2     MT50_H6
6450255 0.141558400 0.941558400 0.098701300 0.688311700 0.602597400 0.244155800
6370619 0.300000000 0.003896104 0.633766200 0.959740300 0.006493506 0.397402600
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.001298701 0.003896104 0.001298701 0.009090909 0.002597403 0.009090909
            MT50_H4     MT50_H5     CS15_H3     CS15_H2     CS15_H1     CS15_H6
6450255 0.281818200 0.283116900 0.098701300 0.496103900 0.219480500 0.318181800
6370619 0.014285710 0.229870100 0.007792208 0.002597403 0.631168800 0.079220780
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.001298701 0.002597403 0.001298701 0.000000000 0.001298701 0.001298701
           CS15_H5     CS15_H4    BZ2.5_H2    BZ2.5_H1    BZ2.5_H3   BZ2.5_H5
6450255 0.32987010 0.822077900 0.342857200 0.200000000 0.045454550 0.64935060
6370619 0.02987013 0.002597403 0.001298701 0.077922080 0.005194805 0.02987013
2600039 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000 0.00000000
2650615 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000 0.00000000
5340672 0.00000000 0.003896104 0.002597403 0.003896104 0.002597403 0.01558442
           BZ2.5_H4    BZ2.5_H6     AN25_H1     AN25_H3     AN25_H2     AN25_H4
6450255 0.292207800 0.659740300 0.437662300 0.202597400 0.333766200 0.329870100
6370619 0.001298701 0.325974000 0.110389600 0.197402600 0.006493506 0.001298701
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.001298701 0.001298701 0.002597403 0.002597403 0.002597403 0.002597403
            AN25_H6     AN25_H5      BA_H1       BA_H2       BA_H3       BA_H4
6450255 0.832467600 0.297402600 0.17532470 0.123376600 0.081818180 0.202597400
6370619 0.332467500 0.011688310 0.26493510 0.002597403 0.012987010 0.001298701
2600039 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000 0.000000000
5340672 0.001298701 0.001298701 0.01038961 0.002597403 0.002597403 0.001298701
              BA_H5       BA_H6     AP5_H3     AP5_H2    AP5_H1      AP5_H6
6450255 0.301298700 0.324675300 0.12597400 0.53636370 0.1038961 0.288311700
6370619 0.136363600 0.124675300 0.16233770 0.43636360 0.3948052 0.020779220
2600039 0.000000000 0.000000000 0.00000000 0.00000000 0.0000000 0.000000000
2650615 0.000000000 0.000000000 0.00000000 0.00000000 0.0000000 0.000000000
5340672 0.003896104 0.003896104 0.06753246 0.07662338 0.1000000 0.002597403
             AP5_H5     AP5_H4     CS12_H2     CS12_H1     CS12_H3     CS12_H5
6450255 0.763636400 0.32467530 0.555844100 0.590909100 0.344155800 0.123376600
6370619 0.050649350 0.03116883 0.002597403 0.081818180 0.324675300 0.032467530
2600039 0.000000000 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.00000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.003896104 0.06103896 0.001298701 0.002597403 0.001298701 0.002597403
            CS12_H4     CS12_H6     CP30_H2    CP30_H1     CP30_H3     CP30_H5
6450255 0.559740200 0.270129900 0.176623400 0.05454545 0.496103900 0.461038900
6370619 0.002597403 0.011688310 0.012987010 0.07792208 0.023376620 0.058441560
2600039 0.000000000 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
5340672 0.003896104 0.001298701 0.003896104 0.02337662 0.003896104 0.003896104
            CP30_H4     CP30_H6    MT100_H1  MT100_H3    MT100_H2    MT100_H4
6450255 0.522077900 0.097402590 0.397402600 0.3857143 0.025974030 0.205194800
6370619 0.005194805 0.070129870 0.088311690 0.4610389 0.036363640 0.003896104
2600039 0.000000000 0.000000000 0.000000000 0.0000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.0000000 0.000000000 0.000000000
5340672 0.001298701 0.002597403 0.005194805 0.6259740 0.002597403 0.003896104
           MT100_H6    MT100_H5     CP20_H2     CP20_H3    CP20_H1     CP20_H5
6450255 0.480519500 0.527272700 0.142857100 0.371428600 0.14545450 0.258441600
6370619 0.166233800 0.238961000 0.002597403 0.190909100 0.20389610 0.025974030
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.00000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.00000000 0.000000000
5340672 0.003896104 0.003896104 0.002597403 0.002597403 0.08571429 0.002597403
            CP20_H6     CP20_H4     AN50_H1     AN50_H3     AN50_H2     AN50_H4
6450255 0.685714300 0.606493500 0.027272730 0.596103900 0.651948000 0.410389600
6370619 0.781818200 0.002597403 0.346753200 0.736363600 0.012987010 0.023376620
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.001298701 0.002597403 0.001298701 0.001298701 0.002597403 0.002597403
            AN50_H6     AN50_H5  CL2.5_H3   CL2.5_H1    CL2.5_H2    CL2.5_H6
6450255 0.451948000 0.454545500 0.1883117 0.52987020 0.301298700 0.497402600
6370619 0.153246800 0.083116880 0.3610390 0.11558440 0.164935100 0.093506490
2600039 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000 0.000000000
5340672 0.001298701 0.003896104 0.1623377 0.04545455 0.001298701 0.003896104
          CL2.5_H4   CL2.5_H5     ND8_H2    ND8_H1     ND8_H3     ND8_H5     ND8_H4
6450255 0.56883110 0.24155840 0.92987010 0.4558442 0.13376620 0.26883120 0.39740260
6370619 0.01688312 0.21298700 0.01558442 0.2454545 0.36103900 0.70779220 0.11948050
2600039 0.00000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000
2650615 0.00000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000
5340672 0.16753250 0.05324675 0.02077922 0.3337662 0.02467532 0.04285714 0.05714286
            ND8_H6     CL1_H1    CL1_H2     CL1_H3     CL1_H4     CL1_H5    CL1_H6
6450255 0.27532470 0.09870130 0.1571429 0.51428570 0.45844160 0.51818180 0.2792208
6370619 0.21168830 0.19740260 0.9818182 0.87402600 0.11948050 0.06103896 0.6480520
2600039 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 0.0000000
2650615 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 0.0000000
5340672 0.01948052 0.06233766 0.3272727 0.01428571 0.05324675 0.03766234 0.2012987
            EE25_H3     EE25_H1     EE25_H2     EE25_H6     EE25_H4     EE25_H5
6450255 0.338961000 0.322077900 0.462337700 0.163636400 0.177922100 0.470129900
6370619 0.033766230 0.153246800 0.005194805 0.111688300 0.006493506 0.032467530
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.001298701 0.001298701 0.001298701 0.001298701 0.003896104 0.003896104
           CH0.5_H3    CH0.5_H1   CH0.5_H2    CH0.5_H4    CH0.5_H5    CH0.5_H6
6450255 0.489610400 0.067532460 0.62727270 0.040259740 0.867532500 0.459740300
6370619 0.227272700 0.270129900 0.68961040 0.001298701 0.087012980 0.737662300
2600039 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000 0.000000000
5340672 0.001298701 0.007792208 0.02077922 0.001298701 0.001298701 0.005194805
           ND15_H3   ND15_H2   ND15_H1    ND15_H6    ND15_H5   ND15_H4     AN75_H1
6450255 0.31428570 0.6389610 0.1311688 0.01298701 0.12467530 0.2207792 0.705194800
6370619 0.14545450 0.6285715 0.2337662 0.36753250 0.65324680 0.1207792 0.414285700
2600039 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.000000000
2650615 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.000000000
5340672 0.03116883 0.5363637 0.1662338 0.02467532 0.05584415 0.1207792 0.006493506
            AN75_H2     AN75_H3     AN75_H4     AN75_H5     AN75_H6 CH0.25_H3
6450255 0.394805200 0.098701300 0.358441600 0.538961100 0.701298700 0.3064935
6370619 0.023376620 0.714285700 0.006493506 0.376623400 0.093506490 0.4740260
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.0000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.0000000
5340672 0.002597403 0.001298701 0.002597403 0.002597403 0.001298701 0.1402597
         CH0.25_H4   CH0.25_H6   CH0.25_H5  AP2.5_H2  AP2.5_H1    AP2.5_H3
6450255 0.18831170 0.223376600 0.328571400 0.2558441 0.3545454 0.375324700
6370619 0.37922080 0.240259700 0.370129900 0.1727273 0.3974026 0.389610400
2600039 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.000000000
2650615 0.00000000 0.000000000 0.000000000 0.0000000 0.0000000 0.000000000
5340672 0.02077922 0.001298701 0.005194805 0.4935065 0.3493507 0.002597403
           AP2.5_H5    AP2.5_H4    AP2.5_H6      C24_H2      C24_H3     C24_H1
6450255 0.885714300 0.272727300 0.224675300 0.188311700 0.535064900 0.27012990
6370619 0.107792200 0.003896104 0.661038900 0.003896104 0.005194805 0.07142857
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.00000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.00000000
5340672 0.002597403 0.050649350 0.001298701 0.002597403 0.002597403 0.02467532
             C24_H5      C24_H6      C24_H4     CP10_H3     CP10_H2     CP10_H6
6450255 0.706493500 0.048051950 0.100000000 0.162337700 0.900000000 0.459740300
6370619 0.196103900 0.901298700 0.005194805 0.163636400 0.002597403 0.611688300
2600039 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
2650615 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
5340672 0.003896104 0.001298701 0.001298701 0.002597403 0.002597403 0.001298701
            CP10_H5   CP40_H1     CP40_H4
6450255 0.677922100 0.2363636 0.283116900
6370619 0.101298700 0.4558442 0.005194805
2600039 0.000000000 0.0000000 0.000000000
2650615 0.000000000 0.0000000 0.000000000
5340672 0.003896104 0.3961039 0.005194805
34471 more rows ...

$Avg_NBEADS
        DMSO_H1 DMSO_H3 DMSO_H2 DMSO_H4 DMSO_H6 DMSO_H5 CH1.5_H1 CH1.5_H2 EE75_H3
6450255      19      25      23      21      20      25       12       20      22
6370619      21      30      31      19      26      13       17       22      27
2600039      22      34      25      22      23      20       22       20      26
2650615      12      25      10      27      23      12       20       26      18
5340672      32      16      21      13      20      20       16       25      19
        EE75_H1 EE75_H2 EE75_H6 EE75_H4 EE75_H5 CH1_H3 CH1_H1 CH1_H2 CH1_H4 CH1_H6
6450255      28      13      11      22      16     26     19     17     25     22
6370619      19      18      28      19      25     20     21     17     30     11
2600039      18      24      17      24      31     17     27     19     25     23
2650615      12      16      15      29      23     13     21     26     22     15
5340672      20      13      18      31      22     17     27     23     24     27
        CH1_H5 ND4_H2 ND4_H3 ND4_H1 ND4_H5 ND4_H6 ND4_H4 BZ5_H2 BZ5_H3 BZ5_H1
6450255     15     26     23     23     15     30     11     24     21     14
6370619     20     16     17     18     24     15     25     25     27     28
2600039     24     28     26     21     19     24     22     23     28     10
2650615     17     20     20     19     17     18     17     13     11     13
5340672     22     16     26     23     23     16     17     17     27     20
        BZ5_H5 BZ5_H6 BZ5_H4 MT75_H1 MT75_H3 MT75_H2 MT75_H4 MT75_H6 MT75_H5
6450255     20     24     20      16      20      28      25      22      27
6370619     21     24     31      32      21      22      23      28      22
2600039     21     16     20      28      24      20      22      30      23
2650615     17     23     21      16      27      19      20      21      26
5340672     27     16     22      25      22      22      24      28      16
        EE50_H3 EE50_H1 EE50_H2 EE50_H6 EE50_H4 EE50_H5 CL5_H3 CL5_H2 CL5_H1 CL5_H6
6450255      12      21      23      18      26      18     13     26     24     16
6370619      28      24      16      18      24      26     21     20     31     21
2600039      28      22      22      18      23       8     18     15     25     19
2650615      22      22      22      17       9      16     18     19     12     19
5340672      18      20      21      18      21      18     33     27     15     20
        CL5_H5 CL5_H4 BZ7.5_H2 BZ7.5_H1 BZ7.5_H3 BZ7.5_H5 BZ7.5_H4 BZ7.5_H6 CS9_H2
6450255     18     26       25       22       15       15       17       23     24
6370619     18     17       20       26       28       13       25       26     23
2600039     19     18       22       16       14       27       17       23     25
2650615     19     13       16       15       24       18       21       24     19
5340672     12     27       25       17       20       19       21       20     21
        CS9_H3 CS9_H1 CS9_H5 CS9_H6 CS9_H4 MT50_H3 MT50_H1 MT50_H2 MT50_H6 MT50_H4
6450255     24     19     24     24     16      20      28      20      21      16
6370619     27     19     20     21     24      23      16      20      22      20
2600039     21     29     32     25     33      27      27      21      25      35
2650615     14     24     22     12     10      16      10      21      24      22
5340672     16     21     20     22     22      13      25      17      16      14
        MT50_H5 CS15_H3 CS15_H2 CS15_H1 CS15_H6 CS15_H5 CS15_H4 BZ2.5_H2 BZ2.5_H1
6450255      28      21      21      17      25      34      17       21       23
6370619      26      25      13      20      33      35      15       29       22
2600039      26      23      15      22      24      19      23       22       20
2650615      17      16      22      24      19      27      22       15       23
5340672      17      25      23      27      25      26      10       18       17
        BZ2.5_H3 BZ2.5_H5 BZ2.5_H4 BZ2.5_H6 AN25_H1 AN25_H3 AN25_H2 AN25_H4 AN25_H6
6450255       21       21       24       26      22      23      30      27      27
6370619       25       29       26       14      24      12      17      22      16
2600039       25       22       14       20      21      21      20      18      23
2650615       24       30       21       24      23      19      22      22      23
5340672       21       17       24       17      17      19      20      15      17
        AN25_H5 BA_H1 BA_H2 BA_H3 BA_H4 BA_H5 BA_H6 AP5_H3 AP5_H2 AP5_H1 AP5_H6
6450255      24    26    23    25    22    22    24     17     15     23     27
6370619      15    22    21    27    18    24    21     22     18     10     22
2600039      29    26    23    18    25    23    17     25     15     25     26
2650615      22    14    15     6    25    21    15     19     27     22     22
5340672      25    24    24    15    18    12    24     21     26     28     16
        AP5_H5 AP5_H4 CS12_H2 CS12_H1 CS12_H3 CS12_H5 CS12_H4 CS12_H6 CP30_H2
6450255     16     26      17      28      17      24      25      14      24
6370619     30     26      21      21      21      20      21      19      18
2600039     21     14      22      23      14      27      14      35      25
2650615     18     21      14      12      23      25      20      27      20
5340672     16     27      17      20      22      19      21      22      17
        CP30_H1 CP30_H3 CP30_H5 CP30_H4 CP30_H6 MT100_H1 MT100_H3 MT100_H2 MT100_H4
6450255      21      22      22      30      26       28       10       16       20
6370619      21      23      19      15      19       23       20       19       18
2600039      22      24      29      23      24       28       32       30       17
2650615      20      17      24      15      21       23       29       18       18
5340672      27      20      26      30      31       22       21       20       21
        MT100_H6 MT100_H5 CP20_H2 CP20_H3 CP20_H1 CP20_H5 CP20_H6 CP20_H4 AN50_H1
6450255       18       15      15      24      20      20      16      24      18
6370619       25       28      26      17      23      20      22      17      27
2600039       25       22      20      23      26      31      31      25      29
2650615       21       27      19      16      21      20      18      26      23
5340672       24       19      19      18      22      17      30      18      22
        AN50_H3 AN50_H2 AN50_H4 AN50_H6 AN50_H5 CL2.5_H3 CL2.5_H1 CL2.5_H2 CL2.5_H6
6450255      24      11      26      25      23       16       12       23       23
6370619      18      14      21      21      26       18       23       29       27
2600039      19      21      20      24      15       18       34       23       27
2650615      25      18      15      18      22       20       18       14       18
5340672      16      26      19      20      22       21       19        9       20
        CL2.5_H4 CL2.5_H5 ND8_H2 ND8_H1 ND8_H3 ND8_H5 ND8_H4 ND8_H6 CL1_H1 CL1_H2
6450255       36       15     18     28     27     20     16     20     19     17
6370619       16       21     24     17     19     15     17     21     17     12
2600039       14       22     28     21     31     26     33     26     21     18
2650615       15       17     15     17     25     15     15     23     17     20
5340672       18       17     23     21     16     16     12     24     18     19
        CL1_H3 CL1_H4 CL1_H5 CL1_H6 EE25_H3 EE25_H1 EE25_H2 EE25_H6 EE25_H4 EE25_H5
6450255     27     21     16     24      18      15      33      27      26      25
6370619     22     23     17     20      20      33      23      20      28      15
2600039     20     20     19     19      19      26      30      19      21      15
2650615     18     16     18     19      12      20      26      22      27      25
5340672     19     28     26     12      12      12      12      21      22      18
        CH0.5_H3 CH0.5_H1 CH0.5_H2 CH0.5_H4 CH0.5_H5 CH0.5_H6 ND15_H3 ND15_H2
6450255       17       19       13       27       21       32      27      20
6370619       22       15       25       28       24       30      17      19
2600039       22       22       17       19       28       24      30      27
2650615       16       24       20       15       19       16      19      18
5340672       20       22       27       25       11       20      19      17
        ND15_H1 ND15_H6 ND15_H5 ND15_H4 AN75_H1 AN75_H2 AN75_H3 AN75_H4 AN75_H5
6450255      30      22      33      28      15      22      20      18      19
6370619      24      24      18      25      30      24      21      19      25
2600039      23      21      17      26      17      27      25      28      29
2650615      25      20      15      16      18      15      18      24      26
5340672      21      26      24      16      25      16      18      32      19
        AN75_H6 CH0.25_H3 CH0.25_H4 CH0.25_H6 CH0.25_H5 AP2.5_H2 AP2.5_H1 AP2.5_H3
6450255      24        27        27        21        14       23       27       21
6370619      21        24        22        26        22       26       20       25
2600039      36        23        28        24        21       16       18       26
2650615      23        13        23        16        15       15       16       23
5340672      17        18        13        15        22       17       29       20
        AP2.5_H5 AP2.5_H4 AP2.5_H6 C24_H2 C24_H3 C24_H1 C24_H5 C24_H6 C24_H4
6450255       14       14       21     22     32     23     16     33     23
6370619       27       27       24     24     27     24     16     16     14
2600039       29       22       29     31     26     21     18     28     27
2650615       19       24       15     15     24     23     28     17     21
5340672       21       20       15     22     19     22     21     19     20
        CP10_H3 CP10_H2 CP10_H6 CP10_H5 CP40_H1 CP40_H4
6450255      15      19      15      15      25      23
6370619      33      16      20      28      23      27
2600039      11      28      28      31      24      27
2650615      18      24      27      11      25      19
5340672      23      19      20      22      13      27
34471 more rows ...

ADD REPLYlink written 5.0 years ago by vas40

> print(Sample)
  [1] "DMSO.1"   "DMSO.3"   "DMSO.2"   "DMSO.4"   "DMSO.6"   "DMSO.5"   "CH1.5.1" 
  [8] "CH1.5.2"  "EE75.3"   "EE75.1"   "EE75.2"   "EE75.6"   "EE75.4"   "EE75.5"  
 [15] "CH1.3"    "CH1.1"    "CH1.2"    "CH1.4"    "CH1.6"    "CH1.5"    "ND4.2"   
 [22] "ND4.3"    "ND4.1"    "ND4.5"    "ND4.6"    "ND4.4"    "BZ5.2"    "BZ5.3"   
 [29] "BZ5.1"    "BZ5.5"    "BZ5.6"    "BZ5.4"    "MT75.1"   "MT75.3"   "MT75.2"  
 [36] "MT75.4"   "MT75.6"   "MT75.5"   "EE50.3"   "EE50.1"   "EE50.2"   "EE50.6"  
 [43] "EE50.4"   "EE50.5"   "CL5.3"    "CL5.2"    "CL5.1"    "CL5.6"    "CL5.5"   
 [50] "CL5.4"    "BZ7.5.2"  "BZ7.5.1"  "BZ7.5.3"  "BZ7.5.5"  "BZ7.5.4"  "BZ7.5.6" 
 [57] "CS9.2"    "CS9.3"    "CS9.1"    "CS9.5"    "CS9.6"    "CS9.4"    "MT50.3"  
 [64] "MT50.1"   "MT50.2"   "MT50.6"   "MT50.4"   "MT50.5"   "CS15.3"   "CS15.2"  
 [71] "CS15.1"   "CS15.6"   "CS15.5"   "CS15.4"   "BZ2.5.2"  "BZ2.5.1"  "BZ2.5.3" 
 [78] "BZ2.5.5"  "BZ2.5.4"  "BZ2.5.6"  "AN25.1"   "AN25.3"   "AN25.2"   "AN25.4"  
 [85] "AN25.6"   "AN25.5"   "DMSO.1"   "DMSO.2"   "DMSO.3"   "DMSO.4"   "DMSO.5"  
 [92] "DMSO.6"   "AP5.3"    "AP5.2"    "AP5.1"    "AP5.6"    "AP5.5"    "AP5.4"   
 [99] "CS12.2"   "CS12.1"   "CS12.3"   "CS12.5"   "CS12.4"   "CS12.6"   "CP30.2"  
[106] "CP30.1"   "CP30.3"   "CP30.5"   "CP30.4"   "CP30.6"   "MT100.1"  "MT100.3" 
[113] "MT100.2"  "MT100.4"  "MT100.6"  "MT100.5"  "CP20.2"   "CP20.3"   "CP20.1"  
[120] "CP20.5"   "CP20.6"   "CP20.4"   "AN50.1"   "AN50.3"   "AN50.2"   "AN50.4"  
[127] "AN50.6"   "AN50.5"   "CL2.5.3"  "CL2.5.1"  "CL2.5.2"  "CL2.5.6"  "CL2.5.4" 
[134] "CL2.5.5"  "ND8.2"    "ND8.1"    "ND8.3"    "ND8.5"    "ND8.4"    "ND8.6"   
[141] "CL1.1"    "CL1.2"    "CL1.3"    "CL1.4"    "CL1.5"    "CL1.6"    "EE25.3"  
[148] "EE25.1"   "EE25.2"   "EE25.6"   "EE25.4"   "EE25.5"   "CH0.5.3"  "CH0.5.1" 
[155] "CH0.5.2"  "CH0.5.4"  "CH0.5.5"  "CH0.5.6"  "ND15.3"   "ND15.2"   "ND15.1"  
[162] "ND15.6"   "ND15.5"   "ND15.4"   "AN75.1"   "AN75.2"   "AN75.3"   "AN75.4"  
[169] "AN75.5"   "AN75.6"   "CH0.25.3" "CH0.25.4" "CH0.25.6" "CH0.25.5" "AP2.5.2" 
[176] "AP2.5.1"  "AP2.5.3"  "AP2.5.5"  "AP2.5.4"  "AP2.5.6"  "C24.2"    "C24.3"   
[183] "C24.1"    "C24.5"    "C24.6"    "C24.4"    "CP10.3"   "CP10.2"   "CP10.6"  
[190] "CP10.5"   "CP40.1"   "CP10.4" 

ADD REPLYlink written 5.0 years ago by vas40

My apologies. Obviously, y2 will not contain target information. Run:

y$targets <- targets

prior to the call to avearrays. This will add the target information to the EList object, such that averaging and removal of duplicates will be reflected in the y2$targets matrix.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Aaron Lun25k
Answer: Including technical and biological replicates in Limma block analysis?
0
gravatar for vas
5.0 years ago by
vas40
Chicago
vas40 wrote:

Dear Aaron,

This is the output from traceback()

5: subsetListOfArrays(object, i, j, IJ = IJ, IX = IX, I = I, JX = JX)
4: `[.EList`(x, , !d)
3: x[, !d]
2: avearrays.EList(y, ID = Sample)
1: avearrays(y, ID = Sample)

ADD COMMENTlink written 5.0 years ago by vas40

You should put this as a reply to my comment, rather than as a separate answer. This keeps the thread a bit more organized. Anyway, I'm having trouble reproducing the error. Just to be sure, what's your sessionInfo() look like?

ADD REPLYlink written 5.0 years ago by Aaron Lun25k
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