[BioC] limma wrongly reading data
piotrek.stepniak at gmail.com
Tue Jun 3 11:22:21 CEST 2008
Thank you for your answer, I have already posted more information
about my problem in response to another email:
Please have a look at it.
Thank you for pointing out that there is a newer version of limma,
however the upgrade did not change anything. If you need more
information please let me know.
2008/6/3 Wolfgang Huber <huber at ebi.ac.uk>:
> Dear Piotr,
> thank you for your report. I suppose that unless you supply (some of) the
> .gpr files that cause your problem, and a more precise description of what
> the problem is, it will be difficult to help you.
> Also, please use the latest release of R and limma. There will be more
> common interest in discussing these than for obsolete versions.
> Best wishes
> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
> Piotr Stępniak a écrit 01/06/2008 23:33:
>> Hello Everyone,
>> I am having problems using limma to analyse my data. It seems that
>> when executing the function read.maimages() over the data it gets read
>> wrongly - the values are taken from first next to right column. So for
>> example under "F543
>> Median" I get "F543 Mean" values and so on, this causes printer layout
>> problem and any other function used on the data to fail...
>> The function to read data looks like this:
>> bialkoRaw<- read.maimages( dir(pattern="gpr"), columns=list(G="F543
>> Median", Gb="B543 Median", R="F633 Median", Rb="B633 Median"),
>> annotation=c("Block", "Column", "Row", "Name", "ID"), row.names=NULL,
>> stringsAsFactors = default.stringsAsFactors())
>> My sessionInfo():
>> R version 2.6.2 (2008-02-08)
>> attached base packages:
>>  grid splines tools stats graphics grDevices utils
>>  datasets methods base
>> other attached packages:
>>  arrayQuality_1.18.0 gridBase_0.4-3 hexbin_1.14.0
>>  convert_1.16.0 RColorBrewer_1.0-2 cluster_1.11.10
>>  arrayMagic_1.16.1 genefilter_1.16.0 survival_2.34-1
>>  marray_1.18.0 vsn_3.6.0 affy_1.16.0
>>  preprocessCore_1.0.0 affyio_1.8.0 Biobase_1.16.3
>>  lattice_0.17-7 limma_2.14.1
>> loaded via a namespace (and not attached):
>>  AnnotationDbi_1.0.6 DBI_0.2-4 RSQLite_0.6-8
>>  annotate_1.18.0 rcompgen_0.1-17 tcltk_2.6.2
>> Does anyone have any idea what might be wrong?
>> I'd appreciate any help.
>> Kind Regards,
>> Piotr Stępniak
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