I have found the reason. Your data file includes control data
with the expression data. Because the control data includes no
information (that's not a problem), lumiR outputted the message. So no
problem for your data file and lumiR output. I will update the code
inputting controlData information to suppress such messages. Thanks!
On Wed, Apr 24, 2013 at 10:50 PM, Atul Kakrana
> Hi Pan,
> You are right the first 100 lines from sample file are read without
> but when try to read whole file than same problem:
> > test <- lumiR('FinalReport.txt', annotationColumn = c('PROBE_ID',
> Inputting the data ...
> Annotation columns are not available in the data.
> Perform Quality Control assessment of the LumiBatch object ...
> I tried options(error=recover) but it did not give any output or
maybe I don't know how to use it. I am attaching the whole file and
hoping a response.
> What I am trying to achieve is that do preprocessing, filter on
p-values and than use 'genefilter' package to collapse multiple
probesets into one using 'rowmedian' function. And use the remaining
probsets for further analysis. I have done this for affymetrix but
trying same for Illumina.
> The attached file is not from public domain.
> On 23-Apr-13 2:05 PM, Pan Du wrote:
> Hi Atul
> I just had a quick try of the example data you sent. It works
> well. Here is my command:
> test <- lumiR('FinalReport_sample.txt', annotationColumn =
> If you still have problems, change the error options and send me
> error messages:
> On Tue, Apr 23, 2013 at 10:49 AM, Atul Kakrana
>> Hi Pan,
>> Thanks for replying. Please see attached file with first 100 lines
>> Awaiting response.
>> On 04/23/2013 11:53 AM, Pan Du wrote:
>> Hi Atul
>> Can you send me to the top 100 rows of your data file? I cannot
>> the reason without seeing your data. Thanks for reporting this!
>> Date: Mon, 22 Apr 2013 13:28:21 -0400
>> From: Atul Kakrana <email@example.com>
>> To: "firstname.lastname@example.org" <email@example.com>
>> Subject: [BioC] Lumi problem - 'Annotation columns not available'
>> Message-ID: <firstname.lastname@example.org>
>> Content-Type: text/plain; charset="ISO-8859-1"
>> Hello All,
>> I am trying to input the Illumina Microarray data using 'lumi' but
>> getting an error:
>> > mydata_test <-
>> Inputting the data ...
>> Inputting the data ...
>> Annotation columns are not available in the data.
>> Perform Quality Control assessment of the LumiBatch object ...
>> This error is not new to me as I had this problem before as well.
>> that time I ignored it and later in analysis used 'lumiMouseAll.db'
>> package for annotations. The final results had incomplete (missing)
>> This time I really need complete annotations and therefore trying
>> import annotations as provided by Beadstudio rather than using
>> 'lumiMouseAll.db'. Please tell me what is the problem as I checked
>> the mentioned columns does exist in rawfile.
>> R version 2.15.3 (2013-03-01)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>  LC_NAME=C LC_ADDRESS=C
>> LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>> attached base packages:
>>  stats graphics grDevices utils datasets methods
>> other attached packages:
>>  lumiMouseIDMapping_1.10.0 illuminaMousev1.db_1.16.1
>> illuminaMousev2.db_1.16.1 lumiMouseAll.db_1.18.0
>> org.Mm.eg.db_2.8.0 calibrate_1.7.1
>>  affyQCReport_1.36.0 lattice_0.20-13
>> farms_1.10.0 MASS_7.3-23
>> genefilter_1.40.0 R2HTML_2.2
>>  affycoretools_1.30.0 KEGG.db_2.8.0
>> affy_1.36.1 GO.db_2.8.0
>> RSQLite_0.11.2 DBI_0.2-5
>>  limma_3.14.4 lumi_2.10.0
>> nleqslv_2.0 Biobase_2.18.0
>> loaded via a namespace (and not attached):
>>  affyio_1.26.0 affyPLM_1.34.0 annaffy_1.30.0
>> AnnotationForge_1.0.3 BiocInstaller_1.8.3 biomaRt_2.14.0
>> Biostrings_2.26.3 Category_2.24.0
>>  colorspace_1.2-1 gcrma_2.30.0 gdata_2.12.0
>> GOstats_2.24.0 gplots_2.11.0 graph_1.36.2
>> grid_2.15.3 GSEABase_1.20.2
>>  gtools_2.7.0 IRanges_1.16.6 KernSmooth_2.23-10
>> Matrix_1.0-11 methylumi_2.4.0 mgcv_1.7-22
>> nlme_3.1-108 parallel_2.15.3
>>  preprocessCore_1.20.0 RBGL_1.34.0 RColorBrewer_1.0-5
>> RCurl_1.95-4.1 simpleaffy_2.34.0 splines_2.15.3
>> stats4_2.15.3 survival_2.37-4
>>  tools_2.15.3 XML_3.95-0.2 xtable_1.7-1
[[alternative HTML version deleted]]