Hi Alison, I guess the data you have does not include the ³BEAD_STDERR² columns, which are required to create LumiBatch object. lumiR will create an ExpressionSet object if the ³BEAD_STDERR² columns are not available in the file. Ask your core facility to output ³AVG_Signal², ³BEAD_STDERR², ³Detection Pval² columns, probably also ³Avg_NBEADS². If there are not many samples, I recommend output all columns BeadStudio can output. Pan On 7/31/08 1:54 PM, "Alison Ziesel" <aziesel@emory.edu> wrote: > Dear Dr. Du, > > I am a graduate student, currently learning to analyze microarray data both > for my own research and for some of our laboratory's collaborations. I've > recently been given data from an Illumina array experiment to analyze, and > would like very much to do so using your lumi package. However, I've been > having difficulties importing the data files provided by our microarray > facility, and suspect that I am either using incomplete or incorrectly > formatted BeadStudio data. When I am able  to import data using lumiR, I am > unable to create a lumiBatch object; rather, I get a generic ExpressionSet > object, which if I understand correctly, cannot take full advantage of the > lumi package for subsequent analysis. > > Here is the sequence of commands I've used to get this far: > >> > library("lumi") >> > library("lumiRatV1") >> > test_read <- lumiR("SampleProbeSignal.txt", lib = "lumiRatV1") >> > test_read > ExpressionSet (storageMode: lockedEnvironment) > assayData: 22523 features, 21 samples >   element names: exprs > phenoData >   sampleNames: 76-PW-1, 76-PW-1a, ..., 76-PW-7b  (21 total) >   varLabels and varMetadata description: >     sampleID: The unique Illumina microarray Id >     label: The label of the sample > featureData >   featureNames: ILMN_1369537, ILMN_1358051, ..., ILMN_1352673 (22523 total) >   fvarLabels and fvarMetadata description: none > experimentData: use 'experimentData(object)' > Annotation: > > > And here is my session info: > >> > sessionInfo() > R version 2.6.2 (2008-02-08) > powerpc-apple-darwin8.10.1 > > locale: > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools     stats     graphics  grDevices utils     datasets methods   base > > > other attached packages: >  [1] lumiRatV1_1.3.1      lumi_1.4.0           annotate_1.16.1 >  xtable_1.5-2 >  [5] AnnotationDbi_1.0.6  RSQLite_0.6-8        DBI_0.2-4 >  mgcv_1.3-29 >  [9] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1 > Biobase_1.16.3 > > > I am not sure if attaching my SampleProbeSignal.txt file will be useful to you > or not. Essentially, what I hope to learn from you is the exact format of file > to request from our microarray facility staff, so that I can proceed with the > lumi package from there. If there is any further information required > regarding my problem I will be happy to provide it. I am very grateful for any > assistance you may be able to provide, and look forward to hearing from you. > > > > Alison Ziesel > Department of Ophthalmology, Emory University > aziesel@emory.edu > > [[alternative HTML version deleted]]

Hello Dr. Du, Thank you so much for your quick reply. One of the files provided to me by our core facility did include BEAD_STDERR (as well as the other columns you mentioned), and I got this error when I attempted to load that file: > probe_file <- lumiR("Probe.txt", lib = "lumiRatV1") Error in mget(targetID, get(paste(lib, "TARGETID2NUID", sep = ""), mode = "environment"), : invalid first argument In addition: Warning message: In formatC(as.numeric(id), width = width, flag = "0", format = "d") : NAs introduced by coercion After receiving this error, the set "probe_file" is not created. When I take a look at Probe.txt using Excel, it's immediately clear that the ARRAY_STDEV column for each array has "NaN" in each cell. In the experimentation, I removed these columns to see what if any effect it had on my attempts to read the file; I received an identical error message to the one above when I attempted to import data lacking ARRAY_STDEV columns. Session info is the same as was provided in the previous email. Thank you so much for your assistance with this, it's greatly appreciated! On Jul 31, 2008, at 3:11 PM, Pan Du wrote: > Hi Alison, > > I guess the data you have does not include the “BEAD_STDERR” > columns, which are required to create LumiBatch object. lumiR will > create an ExpressionSet object if the “BEAD_STDERR” columns are not > available in the file. > > Ask your core facility to output “AVG_Signal”, “BEAD_STDERR”, > “Detection Pval” columns, probably also “Avg_NBEADS”. If there are > not many samples, I recommend output all columns BeadStudio can > output. > > > Pan > > Alison Ziesel Department of Ophthalmology, Emory University aziesel@emory.edu [[alternative HTML version deleted]]