[BioC] QCReport problem

James W. MacDonald jmacdon at med.umich.edu
Sun Jun 3 00:06:25 CEST 2007

Hi Sanchita,

Sanchita Bhattacharya wrote:
> Hi,
> I have a question about running the QCReport funtion in R 2.5. I work with
> HTHgu133 arrays ( High throughput arrays) and I was trying to get the
> QCReport for those arrays. I uploaded HTHgu133Av2 cdf to run this function.
> But still I am getting error which is pasted below:
> Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip
> type: hthgu133acdf
> Error in plot(qc(object)) : error in evaluating the argument 'x' in
> selecting a method for function 'plot

This means that simpleaffy doesn't know about these chips. A hackish way 
around this (not tested, so if it doesn't work, don't blame me ;-D) is 
to over-write the .qcEnv that contains these qc parameters.

 > library(simpleaffy)
 > df1 <- get("alpha", .qcEnv)
 > df2 <- get("qc.probes", .qcEnv)
 > qc3 <- get("spikes", .qcEnv)
 > df1 <- rbind(df1, "hthgu133acdf" = df1[6,])
 > df2 <- rbind(df2, "hthgu133acdf" = df2[6,])
 > df3 <- rbind(df3, "hthgu133acdf" = df3[6,])
 > .qcEnv <- new.env(hash=TRUE)
 > multiassign(c("alpha","qc.probes","spikes"), c(df1, df2, df3), .qcEnv)

Here we are just using the hgu133a chip data which I think should be the 
same (my understanding is the HT chip is just a bunch of the 'regular' 
chips cobbed together). If this works, you could write a little function 
to do it automatically.



> I will appreciate if somebody can help me to debug this problem.
> Thanks,
> Sanchita
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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