On Mon, Jul 27, 2009 at 6:14 PM, Manisha Brahmachary <
mb3058@c2b2.columbia.edu> wrote:

> I am trying to create an eSet with the following data structures:
>
>
>
> pdata is:
>
>
>
>      ABCB7 ABCC1 ABCC4 ABCD1 ABCD3 ABCD4 ABCE1 ABCF1 ABCG1 ABHD14A ABHD14B
> ABHD2 ABHD4 ABHD5 ABHD8 ABL2
>
> X1015     2     2     2     2  2.00     2     2  2.00  2.00    2.00    2.00
> 2     2  2.00     2    2
>
> X1238     2     2     2     2  2.00     2     2  2.00  2.00    2.00    2.00
> 2     2  2.00     2    2
>
> X1433     2     2     2     2  2.00     2     2  2.00  2.00    2.00    2.00
> 2     2  2.00     2    2
>
> X1520     2     2     2     2  2.00     2     2  2.00  2.00    2.00    2.00
> 2     2  2.00     2    2
>
> X1847     2     2     2     2  3.21     2     2  2.00  2.58    2.81    2.81
> 2     2  2.81     2    2
>
> X1870     2     2     2     2  2.00     2     2  2.00  2.00    2.00    2.00
> 2     2  2.00     2    2
>
> X1928     2     2     2     2  2.00     2     2  2.00  2.00    2.00    2.00
> 2     2  2.00     2    2
>
> X2422     2     2     2     2  2.00     2     2  0.93  2.70    2.00    2.00
> 2     2  2.00     2    2
>
>
>
> exprs is:
>
>       X1015 X1238 X1433 X1520 X1847 X1870 X1928 X2422
>
> ABCB7    8.09  8.50  8.12  8.06  7.65  8.59  8.67  7.80
>
> ABCC1   10.86 10.92 10.17 11.14 10.87  9.91 10.72 10.81
>
> ABCC4    6.75  6.49  6.29  5.05  5.37  7.10  6.86  5.90
>
> ABCD1    4.29  7.52  5.13  5.84  5.41  6.49  5.31  5.47
>
> ABCD3   11.48 10.41 10.63  8.86 10.77 10.68 10.90  9.54
>
> ABCD4    8.35  7.58  7.77  7.26  8.15  7.81  7.71  8.27
>
> ABCE1   11.14  9.30 11.32  9.89  9.86 10.97 11.04  9.85
>
> ABCF1    9.22  9.75 10.22  9.47 10.04  9.49  9.79  9.32
>
> ABCG1    6.76  6.73  6.83  6.92  7.58  6.55  5.88  7.28
>
> ABHD14A  7.83  8.69  7.84  8.13  7.61  8.22  7.22  7.87
>
> ABHD14B  9.20 10.35  9.74  9.63  9.10 10.65  9.25  9.50
>
> ABHD2    8.36  8.70  7.73  9.54  9.56  8.83  8.79  9.06
>
> ABHD4    3.76  3.96  3.14  4.30  5.22  4.17  3.99  4.17
>
> ABHD5    5.39  7.43  5.78  7.17  6.71  6.63  6.14  5.95
>
> ABHD8    4.82  6.00  4.89  5.10  5.19  4.89  5.10  5.74
>
> ABL2     7.39  6.76  6.99  7.09  7.80  7.36  7.09  7.12
>
>
>
> Command I use:
>
> phenoData <- new("AnnotatedDataFrame", data=pdata)
>
> eSet <- new("ExpressionSet", exprs=gxp.mat, phenoData=phenoData)
>
>
>
> questions:
>
>
>
> 1.       Can I create a eSet given the above two data structures
> (especially
> my pData)
>
> 2.       When I run this command: phenoData <- new("AnnotatedDataFrame",
> data=pdata)
>
>
>
> I get the following error:
>
>
>
> Error in value[[3]](cond) :
>
>  AnnotatedDataFrame 'data' is class 'matrix' but should be or extend
> 'data.frame'
>

It appears that your 'pdata' data structure is a matrix.  You need to have a
data.frame.  So, doing this should work, I think:

phenoData <- new("AnnotatedDataFrame",data=data.frame(pdata))

I didn't test this, so let us know if it doesn't work for you.

Sean


>
>  AnnotatedDataFrame 'initialize' could not update varMetadata:
>
>  perhaps pData and varMetadata are inconsistent?
>
>
>
> Is this because my pdata is not in the correct format. Can somebody help me
> explain this error?
>
>
>
> Thanks
>
> manisha
>
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