[BioC] Analyze Single Color Agilent Microarray Data

[Sean Davis]

Thanks, Srikanth, for the details.  I think that the input that you
have gotten already probably sums things up--your best bet is to load
things separately (the two different platforms) and then combine them
in R.  I do not have a script or know of a simple command to do so.
Whether or not the data are going to be comparable across platforms is
another question that may or may not be important, depending on your
experimental design.

As an aside, you are running a fairly old version of R, so you might
consider updating to a newer version.

In the end, I do not have a direct answer for you--sorry.

Sean


On Wed, Aug 3, 2011 at 11:18 AM, Srinivas M. Srikanth
<srikanth at ibioinformatics.org> wrote:
> Hi Sean,
>
> I used following commands to load the files in R. I created a target.txt
> file with content as
> SerialNumber FileName Condition
> 1 Normal1.txt Normal
>
>>library(limma)
>>target<-readTargets()
>>RG<-read.maimages(target,(targets,columns = list(G = "gMedianSignal", Gb =
> "gBGMedianSignal", R = "gProcessedSignal",Rb = "gIsPosAndSignif"),
> annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName")))
> I used some values of R and Rb
>
> After it reads first 18 files it throws the message:
>
> Read Normal18.txt
> Read Wles1.txt
> Read Wles2.txt
> Error in RG[[a]][, i] <- obj[, columns[[a]]] :
>  number of items to replace is not a multiple of replacement length
>
>
>
> The sessionInfo() gives:
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] limma_3.4.5
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0
>
>
> Please help.
>
> Regards,
> Srikanth
>
> On Wed, Aug 3, 2011 at 6:22 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> Hi, Srikanth.
>>
>> Please always provide the code you are using (cut-and-paste), the
>> error message, and sessionInfo() when asking for help.  That will help
>> the list members to more easily figure out what the problem might be.
>>
>> Sean
>>
>>
>> On Wed, Aug 3, 2011 at 8:49 AM, Srinivas M. Srikanth
>> <srikanth at ibioinformatics.org> wrote:
>> > Hi all,
>> >
>> > I have data from single color agilent array exposed and unexposed to
>> drug.
>> > The exposed data is from 1x44 platform and unexposed from 4x44k. When i
>> try
>> > limma and load the files using read.maimages i get the error:
>> >
>> > Error in RG[[a]][, i] <- obj[, columns[[a]]] :
>> >  number of items to replace is not a multiple of replacement length
>> >
>> > Please help me with this. How can load and perform analysis on this data.
>> >
>> > Regards,
>> > Srikanth
>> >
>> > --
>> > Srinivas M. Srikanth
>> > Ph.D. Student
>> > Institute of Bioinformatics
>> > Discoverer, 7th Floor,
>> > International Technology Park,
>> > Bangalore, India
>> > Mob:+917259692031
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
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>> >
>>
>
>
>
> --
> Srinivas M. Srikanth
> Ph.D. Student
> Institute of Bioinformatics
> Discoverer, 7th Floor,
> International Technology Park,
> Bangalore, India
> Mob:+917259692031
>
>        [[alternative HTML version deleted]]
>
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