[BioC] limma and marray data import problem
piotrek.stepniak at gmail.com
Thu Jun 5 09:45:52 CEST 2008
Thank you VERY much for all your answers. One more question and I
should be able to proceed with my analysis:
>> Error: dims [product 2641] do not match the length of object 
>> In addition: Warning message:
>> In samplesub & which & subset & good :
>> longer object length is not a multiple of shorter object length
>> Which is because the array has 36 grids instead of 40 (it is not a
>> full rectangle). Is there a way to go around this situation? Maybe I
>> can set a grid number value?
> There is no way to set the print layout in limma. limma strictly assumes
> complete arrays. You'd have to pad out your data object with NAs for the
> other 4 grids if you want to use print layout functions in limma.
> You do not need the layout to create MA-plots or to loess normalize.
Could you please advice on the best way to pad out the object with
NAs? I tried this:
bialkoRaw[2641:3240,]<- read.maimages( targets$FileName,
columns=list(G="Ch1\ Median", Gb="Ch1\ B\ Median", R="Ch2\ Median",
Rb="Ch2\ B\ Median"), sep=",", na.strings="NA", blank.lines.skip =
and I did not get any additional columns or rows written.
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