[BioC] limma wrongly reading data

[Piotr Stępniak]

Dear Wolfgang,

Thank you for your answer, I have already posted more information
about my problem in response to another email:
http://article.gmane.org/gmane.science.biology.informatics.conductor/18224/match=error+if+is+int+totalPlate+argument+length+zero

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.

Kind Regards,
Piotrek

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
>
> ------------------------------------------------------------------
> 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)
>> i486-pc-linux-gnu
>>
>> locale:
>> C
>>
>> attached base packages:
>>  [1] grid      splines   tools     stats     graphics  grDevices utils
>>  [8] datasets  methods   base
>>
>> other attached packages:
>>  [1] arrayQuality_1.18.0  gridBase_0.4-3       hexbin_1.14.0
>>  [4] convert_1.16.0       RColorBrewer_1.0-2   cluster_1.11.10
>>  [7] arrayMagic_1.16.1    genefilter_1.16.0    survival_2.34-1
>> [10] marray_1.18.0        vsn_3.6.0            affy_1.16.0
>> [13] preprocessCore_1.0.0 affyio_1.8.0         Biobase_1.16.3
>> [16] lattice_0.17-7       limma_2.14.1
>>
>> loaded via a namespace (and not attached):
>> [1] AnnotationDbi_1.0.6 DBI_0.2-4           RSQLite_0.6-8
>> [4] 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
>