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S4 Object Older Than Version 2.4.0 : Please Recreate It

Hi, I have got a bioconductor package, and I am trying to get it to work on my own data; to have a reference, I run the example given in the doc of the package (that contains its own data), but I am blocked with the following message:

Warning :
1: 'human' seems to be an S4 object older than version 2.4.0 : please recreate it.

(translated from french).

The package is truncateCDF (used in the study Nuc.Acids Res; 2005; v.33, p.e111), to generate a new cdf file truncated from unwanted probes.

The object created with data() is an AffyBatch object. But I have no indication concerning the package/software that was older than version 2.4; it could be Bioconductor, Biostrings, Biobase; not affy, that contains the AffyBatch class, and is presently at version 1.34.

My question: how I could rescue the data from human to save it in an up to date S4 object ?

bioconductor
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written by Mycroft34 • Mycroft34

Could you please edit your question to include the output of sessionInfo()? If "human" is an AffyBatch, you can create your own (from your own data) by using the ReadAffy function in the affy package. Have you tried doing that?

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written by Sean Davis Sean Davis

Sorry forgetting that point; here is the result:

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8    LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] truncateCDF_1.0       affy_1.34.0           hgu133plus2cdf_2.10.0 AnnotationDbi_1.18.1  Biobase_2.16.0       
[6] BiocGenerics_0.2.0   

loaded via a namespace (and not attached):
[1] affyio_1.24.0         BiocInstaller_1.4.7   DBI_0.2-5             IRanges_1.14.4        preprocessCore_1.18.0
[6] RSQLite_0.11.1        stats4_2.15.1         tools_2.15.1          zlibbioc_1.2.0

About using my own AffyBatch object, yes, I tried it with two different CEL files, from the same chip (hgu133plu2), and I got different results with the same mask file; is that expected, given that the CEL files are just result files from which to exclude some probesets ? I thought I would get a cdf environment reflecting the chip composition minus the masked probesets, independently of the CEL files !

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written by Mycroft34 • Mycroft34

By the way, I looked more closely to my results, and what I said is not completely true; the remaining probesets are the same, but the excluded probesets are different; so I might have done something wrong. So your suggestion is good, and I used it since then. So I will close this thread.

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written by Mycroft34 • Mycroft34

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