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' 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 [[alternative HTML version deleted]]

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 > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]