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 [[alternative HTML version deleted]]

Hi Amy, These functions are not exported at the user level, but you can find them in parseMAGE.r if you download the source files. Anyway, I looked into this problem and indeed it's not loading because the label column for this experiment is missing and a lot of the reasoning inside the code depends on this column. Nevertheless, I fixed this error to bypass the column and still the experiment failed to load because it couldn't recognise the data file's format. This is a methylation experiment, so not a common one. I would be interested to know what technology is used to produce these data files. Your best bet is to load this experiment with the processed data, which is luckily provided for this experiment. I'll deploy a couple of fixes and hopefully you'll be able to load it via procset function. I'll let you know as soon as I deploy the fixes. (which is very soon) Thanks Ibrahim On 11 Mar 2013, at 19:34, Amy Vandiver <amyruthvandiver@gmail.com> wrote: > 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. > > > > > > > > > -- > Amy Ruth Vandiver > MSII, GSIII > Johns Hopkins School of Medicine, MD-PhD Program > [[alternative HTML version deleted]]