[BioC] shuffle the sample names of an expressionSet

[Al Tango]

Thanks, Martin,
I did find an error in my subsequent process. But your reply is really
helpful. I was calculating p-values of analysis using limma.
AT

On Mon, Nov 10, 2008 at 12:31 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Hi Al --
>
> "Al Tango" <time.is.flying at gmail.com> writes:
>
>> Hi, all, I want to randomly shuffle sample names in an object of
>> expressionSet, aiming
>> to perform permutation test. I did as follows, but the following test
>> result remained unchanged (When I shuffled the original data file
>> names before 'ReadAffy()' , the result did change). So it must be
>> wrong; what's the way please?  Thanks to everybody who help / has
>> helped me.
>> e.g.
>>
>> library(affy)
>> eset=rma(ReadAffy(filenames=c('sample1.CEL','sample2.CEL','sample3.CEL'))
>>
>> # below was what I did to shuffle sample names
>>
>>
>
> This
>
>> data(sample.ExpressionSet)
>> obj1 <- obj <- sample.ExpressionSet
>> sampleNames(obj1) <- sample(sampleNames(obj))
>
> shuffles exprs and phenoData names.
>
>> head(exprs(obj), 2)
>                      A        B        C        D       E       F        G
> AFFX-MurIL2_at  192.742  85.7533 176.7570 135.5750 64.4939 76.3569 160.5050
> AFFX-MurIL10_at  97.137 126.1960  77.9216  93.3713 24.3986 85.5088  98.9086
>                      H       I        J       K       L       M       N
> AFFX-MurIL2_at  65.9631 56.9039 135.6080 63.4432 78.2126 83.0943 89.3372
> AFFX-MurIL10_at 81.6932 97.8015  90.4838 70.5733 94.5418 75.3455 68.5827
>                      O       P        Q       R       S       T         U
> AFFX-MurIL2_at  91.0615 95.9377 179.8450 152.467 180.834 85.4146 157.98900
> AFFX-MurIL10_at 87.4050 84.4581  87.6806 108.032 134.263 91.4031  -8.68811
>                       V       W        X       Y        Z
> AFFX-MurIL2_at  146.8000 93.8829 103.8550 64.4340 175.6150
> AFFX-MurIL10_at  85.0212 79.2998  71.6552 64.2369  78.7068
>> head(exprs(obj1), 2)
>                      S        G        W        L       C       B        I
> AFFX-MurIL2_at  192.742  85.7533 176.7570 135.5750 64.4939 76.3569 160.5050
> AFFX-MurIL10_at  97.137 126.1960  77.9216  93.3713 24.3986 85.5088  98.9086
>                      N       Q        O       K       R       U       J
> AFFX-MurIL2_at  65.9631 56.9039 135.6080 63.4432 78.2126 83.0943 89.3372
> AFFX-MurIL10_at 81.6932 97.8015  90.4838 70.5733 94.5418 75.3455 68.5827
>                      M       Z        E       F       Y       D         V
> AFFX-MurIL2_at  91.0615 95.9377 179.8450 152.467 180.834 85.4146 157.98900
> AFFX-MurIL10_at 87.4050 84.4581  87.6806 108.032 134.263 91.4031  -8.68811
>                       T       P        X       A        H
> AFFX-MurIL2_at  146.8000 93.8829 103.8550 64.4340 175.6150
> AFFX-MurIL10_at  85.0212 79.2998  71.6552 64.2369  78.7068
>> head(pData(obj), 2)
>     sex    type score
> A Female Control  0.75
> B   Male    Case  0.40
>> head(pData(obj1), 2)
>     sex    type score
> S Female Control  0.75
> G   Male    Case  0.40
>
> but I think it is just a tidier way of doing what you already
> did. Perhaps what you meant to do was to shuffle some aspects of
> phenoData, e.g.,
>
>> obj1 <- obj
>> pData(obj1)[["type"]] <- sample(pData(obj1)[["type"]])
>> head(pData(obj), 5)
>     sex    type score
> A Female Control  0.75
> B   Male    Case  0.40
> C   Male Control  0.73
> D   Male    Case  0.42
> E Female    Case  0.93
>> head(pData(obj1), 5)
>     sex    type score
> A Female    Case  0.75
> B   Male    Case  0.40
> C   Male    Case  0.73
> D   Male Control  0.42
> E Female    Case  0.93
>
> ? What are you doing that you would like to see the permutation of?
>
> Martin
>
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>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>