[BioC] Agi4x44PreProcess for miRNA data

[Marten Jäger]

Hi Yong, hi Petro,

thanks for your replies. I did as Yong suggested. Removed the stop point
for "Sequence and chr_coord" and additionally set
"dd$genes=ddaux$genes[,c(4:8)]" like Petro said. This way the data reading
works.
Unfortunately the mapping (due to a missing annotation database) as the
filtering doesn't work (I know that this isn't the right annotation
package):


> ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE,
isfound = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE,
+ NonUnifOL = T, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75,
limSAT = 75, limPopnOL = 75, limNonUnifOL = 75,
+ limNAS = 100, makePLOT = F, annotation.package = "mgug4122a.db",
flag.counts = T, targets)
FILTERING PROBES BY FLAGS


FILTERING BY ControlType FLAG
Error in data.frame(PROBE_ID, as.character(probe.chr),
as.character(probe.seq),  :
  arguments imply differing number of rows: 11540, 0


So I tried to modify the line in the source code by removing all sequence
related lines in the "write.control.out"-function:

...
#probe.seq=ddFILT$genes$Sequence
...
result=data.frame(PROBE_ID,as.character(probe.chr),
	as.character(GENE_ID),
	as.character(gene.sym),as.character(gene.num),
	as.character(gene.des),values)
colnames(result)=c("PROBE","Probe Chr-Coord",
	"ACCNUM","SYMBOL","ENTREZID","DESCRIPTION",paste(g2,g1,sep=" - "))

...

But I still get the above error. Did I miss something or did I look in the
wrong function?

Thanks.

Marten


> The function read.AgilentFE has not been designed to directly read data
> from
> miRNA. The error message you get is due to the fact that I included on
> purpose a stop point if the "Sequence and chr_coord" cannot be found in
> the
> input data set, in order to avoid using the function to read other data
> different from the one that the function is expecting to get. You can use
> this function, instead, which is similar to read.AgilentFE :
>
> read.microRNA.AgilentFE <- function(targets){
>  if (!is(targets, "data.frame")){
>         stop("'targets' must be a data.frame")
>  }
>   ddaux=read.maimages(files=targets$FileName,source="agilent",
>             other.columns=list(IsGeneDetected="gIsGeneDetected",
>             IsSaturated="gIsSaturated",
>             IsFeatNonUnifOF="gIsFeatNonUnifOL",
>             IsFeatPopnOL="gIsFeatPopnOL",
>             ChrCoord="chr_coord",
>             BGKmd="gBGMedianSignal",
>             BGKus="gBGUsed"),
>           columns=list(Rf="gTotalGeneSignal",
>             Gf="gTotalProbeSignal",
>             Rb="gMeanSignal",
>             Gb="gProcessedSignal"),
>           verbose=T,sep="\t",quote="")
>         dd=new("RGList")
>                 dd$R=ddaux$R
>                 dd$G=ddaux$G
>                 dd$Rb=ddaux$Rb
>                 dd$Gb=ddaux$Gb
>                 dd$targets=ddaux$targets
>                 dd$genes=ddaux$genes[,c(4,5,6)]
>                 dd$other=ddaux$other
>         rm(ddaux)
>   cat("","\n")
>   cat("  RGList:","\n")
>   cat(" dd$R:  'gTotalGeneSignal' ","\n")
>   cat(" dd$G:  'gTotalProbeSignal' ","\n")
>   cat(" dd$Rb:  'gMeanSignal' ","\n")
>   cat(" dd$Gb:  'gProcessedSignal' ","\n")
>   cat("","\n")
> return(dd)
> } # end function
>
> HTH
>
> pedro
>
>
>
> Hi all,
>
> is there any way to get the Agi4x44PreProcess package working with Agilent
> miRNA data? I have a target object pointing at Agilent txt files
> containing miRNA data. Reading mRNA data is no problem. For miRNA data I
> get the following error:
>
>> dd=read.AgilentFE(targets, makePLOT=FALSE)
> Read ***.txt
> Read ***.txt
> ...
> INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord
> SCANN THE DATA USING AFE 9.5.3.1
> Error in read.AgilentFE(targets, makePLOT = FALSE) :
>    the script will stop now
>
> Any suggestions?
>
> 	[[alternative HTML version deleted]]
>
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