[BioC] Error message (probably) from AffyBatch.R when using a modified CDF

[James W. MacDonald]

Hi Hugh,

On 1/23/2013 4:06 PM, Hugh Shanahan wrote:
> We are writing a new R package to construct CDF's with particular subsets of probes removed. We are building the CDF packages using a modification of makecdfenv.
> Up until recently, everything has been working fine when we update the CDF library name of an expression set, i.e.
>> raw<- ReadAffy()
>> raw at cdfName<- "hgu133ag4"
>> eSet<- rma(raw)
> Having upgraded to R 2.15.2 and now using the most up to date libraries of bioconductor 2.10 (i.e. doing a clean install on a new (Windows) machine generates an error
> which has cropped over the years, namely if we try to run a normalisation step (such as above) then we get the following error (the same error occurs with other normalisations such as rma) :-
>
>> eSet<- rma(raw)
>
> Attaching package: hgu133ag4cdf
>
> The following object(s) are masked from package:hgu133acdf:
>
>      i2xy, xy2i
>
> Error in ans[[i]][, i.probes] : incorrect number of dimensions
>
> The problem appears to occur in indexProbes which is part of the affy package (AffyBatch.R to be precise), which first gets the environment associated with the expression set,
>
> envir<- getCdfInfo(object)
>
> genenames<- ls(envir)
>
> ans<-  mget(genenames, envir, ifnotfound=NA)
>
> so that ans should be a list with names of affy id's and each entry is a two column data frame with entries for the pm and mm probe locations.
>
> The only possibility when the error is occurring is when the following is called
>
> tmp<- as.vector(ans[[i]][, i.probes])
>
> which suggests that ans is not in this format when it gets to this line. The problem is, I can't reproduce the error if I use the source code of AffyBatch.R .
> Any ideas on how I can check that this hypothesis is correct ? Any ideas how I can fix this ? It looks as if this error has occurred a number of times over the years, but there never seems to be a complete solution...

I don't know what you mean by 'I use the source code of AffyBatch.R'.

Anyway, there are at least two things you can do. First,

ans <- mget(ls(hgu133ag4cdf), ifnotfound = NA)
table(sapply(ans, nrow))

and see if you have any probesets with < 2 rows.

Or you can use

options(error = recover)

and then do whatever will trigger the error. You will then be given a 
choice of frames to enter. You can enter each one and see what e.g. 
i.probes, and ans[[i]] look like, which might help figure out what the 
problem is.

Best,

Jim



>
> Many thanks
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099