[BioC] nsFilter error

[Thomas Lo]

Hi Seth,

Thanks very much for your reply!  Here is what I got from traceback():

> traceback()
6: switch(storage.mode, environment = , lockedEnvironment = {
       aData <- new.env(parent = emptyenv())
       if (missing(i)) 
           for (nm in ls(orig)) aData[[nm]] <- orig[[nm]][, j, ..., 
               drop = drop]
       else {
           if (missing(j)) 
               for (nm in ls(orig)) aData[[nm]] <- orig[[nm]][i, 
                   , ..., drop = drop]
           else for (nm in ls(orig)) aData[[nm]] <- orig[[nm]][i, 
               j, ..., drop = drop]
       }
       if ("lockedEnvironment" == storage.mode) 
           assayDataEnvLock(aData)
       aData
   }, list = {
       if (missing(i)) 
           lapply(orig, function(obj) obj[, j, ..., drop = drop])
       else {
           if (missing(j)) 
               lapply(orig, function(obj) obj[i, , ..., drop = drop])
           else lapply(orig, function(obj) obj[i, j, ..., drop = drop])
       }
   })
5: eset[haveID, ]
4: eset[haveID, ]
3: requireID(eset, "ENTREZID")
2: nsFilter(exset)
1: nsFilter(exset)

Is the output informative?  I have just tried the same procedure with an
independent data set, and that produced the same error.  However, if I read
the data in using ReadAffy() before performing gcrma(), then nsFilter()
appears to work fine.  So perhaps something that is not compatible between
the justGCRMA() output and nsFilter()?

Many thanks!

Thomas


-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Tuesday, July 10, 2007 4:35 AM
To: Thomas Lo
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] nsFilter error

Hi Thomas,

"Thomas Lo" <thom.lo at cuhk.edu.hk> writes:
> I have performed a GCRMA normalization with my Affy data, and then tried
the
> 'nsFilter' function from the 'genefilter' package but got an error message
> as follows.  Help much appreciated.  Thanks.

>> filterAns <- nsFilter(exset)
>
> Error: no 'dimnames' attribute for array

Hmm, I haven't been able to reproduce this.  Can you try calling
traceback() after the error message appears and sending the output?

Also, if you are able to share the data, I could try reproducing
here.  If the data is sharable, perhaps you can save the exset object
using save() (and compress=TRUE)  and post it on a web/ftp that I can
download from?

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org