[BioC] AgiMicroRna problem

[Paulo Nuin]

Thanks a lot. I will try this.

Cheers
Paulo


On 2011-02-01, at 5:00 AM, Pedro Lopez-Romero wrote:

> 
> Hi Pablo,
>  
> The function "read.maimages" is no longer used by AgimicroRna.
> "read.maimages" creates an object of class RGList with element names: R, Rb, G, Gb, etc ..., that are proper for two-channel arrays. To make the names more intuitive for the analysis of microRna arrays, I have introduced some changes and now, AgimicroRna creates an object of class uRNAlist with the names:
> "TGS" for the "gTotalGeneSignal",
> "TPS" for the "gTotalProbeSignal",
> "meanS" for the "gMeanSignal",
> "procS" for the "gProcessedSignal".
> 
> If you use "read.maimages" you will create an object that is no longer available in AgimicroRna, and that´s the error you´ve got.
> 
> Please, to read the data use the fucntion:  readMicroRnaAFE(targets,verbose=FALSE).
> 
> Please have a look at the help of readMicroRnaAFE and at the vignette file (to see the changes)
> For a quick look of the new characteristics of AgiMicroRna, please, have a look as well at: "Lopez-Romero P. Pre-processing and differential expression analysis of Agilent microRNA arrays
> using the AgiMicroRna Bioconductor library. BMC Genomics 2011, 12:64".
> p.- 
> 
> 
> 
> On Sun, Jan 30, 2011 at 1:03 AM, Paulo Nuin <nuin at genedrift.org> wrote:
> Hi
> 
> We're trying to analyse some Agilent microRNA chips with AgiMicroRna without much success. Our chips are V1 and I saw in the documentation that the package is intended to V2. Anyway, we were able to work around the columns issue, but know we are stuck on another problem.
> 
> Our dataset is composed of 30 chips, each one from a different sample. Eleven of those 30 are one treatment, while the remainder 19 are in another treatment. We created a targets file as specified by the manual with 4 columns:
> 
> Filename Treatment GErep Subject
> fileA           A               1               1
> fileB           A               1               2
> fileC           B               2               3
> fileD           B               2               4
> ....                    ...             ...             30
> 
> 
> We were able to read the images into a variable using
> 
> dd=read.maimages(files=targets$FileName,source="agilent", columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal",
> Rb="gTotalGeneSignal", Gb="gProcessedSignal"), other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated",
> IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", probe_mappings="probe_mappings", BGKmd="gBGMedianSignal",
> BGKus="gBGUsed"), annotation = c( "ControlType","ProbeName","GeneName"), verbose=TRUE,sep="\t",quote="")
> 
> names(dd$others) will output
> 
> names(dd$other)
> [1] "gIsGeneDetected"  "gIsSaturated"     "gIsFeatNonUnifOL" "gIsFeatPopnOL"    "gBGMedianSignal"
> 
> But when we run the rmaMicroRna with
> 
> ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE)
> 
> we get the following error:
> 
> Error in split.default(0:(length(pNList) - 1), pNList) :
>  Group length is 0 but data length > 0
> 
> Any help is very appreciated.
> 
> Thanks in advance
> 
> Paulo Nuin
> 
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