[BioC] Problem reading ArrayVision files

[Gordon K Smyth]

Dear Michael,

> Date: Mon, 2 Apr 2007 13:44:50 -0400
> From: "michael waisberg" <waisberg at gmail.com>
> Subject: [BioC] Problem reading ArrayVision files
> To: bioconductor at stat.math.ethz.ch
>
> Hello,
>
> I've been trying to read and analyze some ArrayVision filesusing LIMMA and I
> always get the same problem. I am using R 2.2.1 and I updated my LIMMA to
> the last version today.

Actually you're using a version of R which is about 15 months old, so you're getting an older
version of limma as well.  The only way to get the latest version of limma is to use the current
version of R.

I don't know what problem you have here exactly, without knowing your limma version and without
seeing your input files.  I can tell you that the reading of arrayvision files was broken by the
introduction of colClasses into read.maimages() in limma 2.3.1 on 15 October 2005.  colClasses
greatly speaded up reading for most image analysis programs, but caused problems for a couple of
the less common non-standard formats including ArrayVision.

If you like, you can send me some of your input files and I'll continue to work on getting
ArrayVision up again in limma.

Best wishes
Gordon

> So far my code is very simple (the errors follow
> below the code causing it):
>
>> targets <- readTargets("targets.txt")
>> data <- read.maimages(targets$FileName, source="arrayvision")
>
> Read 01_WG_WR_600_900_flag.txt
> Read 02_PG_PR_650_900_flag.txt
> Read 03_PG_PR_650_900_flag.txt
> Read 26_WG_WR_0651_flag.txt
> Read 28_WG_WR_670_900.txt
> Read 04_PG_PR_650_800.txt
> Read 05_PG_PR_650_900.txt
> Warning message:
> number of items read is not a multiple of the number of columns
>
>> data$genes <- readGAL("cere32pinsJAN04.gal")
>> data$printer <- getLayout(data$genes)
>> MA<- normalizeWithinArrays(data,  method="l")
>> library(convert)
>> data.marray <- as(data, "marrayRaw")
>
> Error in checkSlotAssignment(object, name, value) :
> assignment of an object of class "integer" is not valid for slot 'maGf' in
> an object of class "marrayRaw"; is(value, "matrix") is not TRUE
>
> When I try to normalize the data using a printtip method as for instance:
>>MA<- normalizeWithinArrays(data)
> I get the following error:
> Error in switch(method, loess = { : printer layout information does not
> match M row dimension
>
> The targets.txt file is like this:
> SlideNumber    FileName    cy3    cy5
> 01    01_WG_WR_600_900_flag.txt    WR    WG
> 02    02_PG_PR_650_900_flag.txt    PR    PG
> 03    03_PG_PR_650_900_flag.txt    PR    PG
> 26    26_WG_WR_0651_flag.txt    WG    WR
> 28    28_WG_WR_670_900.txt    WG    WR
> 04    04_PG_PR_650_800.txt    PG    PR
> 05    05_PG_PR_650_900.txt    PG    PR
>  Anyone can help me?
>
> Best regards,
> --
> Michael Waisberg
> R. Nicaragua 443/701, Sion
> Belo Horizonte, MG
> Brazil
> 30320-050
>
>
> _________________________________________
> "I do not fear computers. I fear the lack of them."
> Isaac Asimov