Hello,
I've been trying to access Array Expression data using the Array Expression
Package, however I am running into an error, seemingly due to the format of
the SDRF file. I have been trying to run through the ae2bioc function line
by line (ae2bioc) to determine if I can work around this error, however
many of the called functions (readPhenoData, getSDRFcolumn, etc.) can not
be found.  Am I missing a specific package containing these functions? Is
there a way to work around the original error?
Thank you,
Amy

*My script:*

source("http://bioconductor.org/biocLite.R")

biocLite("ArrayExpress")

library("ArrayExpress")

AEset=ArrayExpress("E-MTAB-202")

*Error:*

Error in .subset2(x, i, exact = exact) :

  attempt to select less than one element

In addition: Warning message:

In readPhenoData(sdrf, path) :

  ArrayExpress: Cannot find 'Label' column in SDRF. Object might not be
created correctly.

*SessionInfo:*

R Under development (unstable) (2013-03-10 r62201)

Platform: x86_64-unknown-linux-gnu (64-bit)


locale:

 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C

 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915

 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915

 [7] LC_PAPER=C                     LC_NAME=C

 [9] LC_ADDRESS=C                   LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C


attached base packages:

[1] parallel  stats     graphics  grDevices datasets  utils     methods

[8] base


other attached packages:

 [1] minfiLocal_0.1.20

 [2] minfiData_0.3.1

 [3] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3

 [4] IlluminaHumanMethylation450kmanifest_0.4.0

 [5] bumphunter_0.99.33

 [6] iterators_1.0.6

 [7] foreach_1.4.0

 [8] minfi_1.5.3

 [9] Biostrings_2.27.11

[10] GenomicRanges_1.11.35

[11] IRanges_1.17.35

[12] reshape_0.8.4

[13] plyr_1.8

[14] lattice_0.20-13

[15] limma_3.15.14

[16] ArrayExpress_1.19.0

[17] Biobase_2.19.3

[18] BiocGenerics_0.5.6

[19] BiocInstaller_1.9.6


loaded via a namespace (and not attached):

 [1] affy_1.37.4           affyio_1.27.1         beanplot_1.1

 [4] codetools_0.2-8       DNAcopy_1.33.1        doRNG_1.5

 [7] grid_3.1.0            illuminaio_0.1.5      itertools_0.1-1

[10] MASS_7.3-24           matrixStats_0.6.2     mclust_4.0

[13] multtest_2.15.0       nor1mix_1.1-3         preprocessCore_1.21.1

[16] RColorBrewer_1.0-5    R.methodsS3_1.4.2     siggenes_1.33.1

[19] splines_3.1.0         stats4_3.1.0          survival_2.37-4

[22] tools_3.1.0           XML_3.95-0.2          zlibbioc_1.5.0




-- 
Amy Ruth Vandiver
MSII, GSIII
Johns Hopkins School of Medicine, MD-PhD Program

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