[BioC] QCReport problem

James W. MacDonald jmacdon at med.umich.edu
Sun Jun 3 00:26:08 CEST 2007

James W. MacDonald wrote:
> Hi Sanchita,
> Sanchita Bhattacharya wrote:
>>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 should probably elaborate a bit here.

The .qcEnv is a little environment containing three data.frames that 
hold certain data that simpleaffy uses. What I show here is hackish 
because you will just be over-writing this env with one containing the 
data you need, and this will not persist beyond the current R session.

Slightly less hackish would be to get the sources for simpleaffy, create 
the env as above, save it, replace the one that comes with simpleaffy 
and re-install. This is slightly more work, and even more if you are on 
Windows and not set up to build packages. However, the changes you made 
would be persistent over different R sessions until you upgrade simpleaffy.

Even less hackish would be to make the env as described above and then 
contribute it to Crispin Miller, the maintainer of simpleaffy. This way 
your changes would persist in perpetuity and others would benefit as well.



> Best,
> Jim
>>I will appreciate if somebody can help me to debug this problem.
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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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