Question: Updated Affy: Readaffy Has Changed And Breaks My Pipeline!
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gravatar for Bdh_Dtu
8.0 years ago by
Bdh_Dtu20
Denmark
Bdh_Dtu20 wrote:

I have created a pipeline for some colleagues which automates some gene chip analysis. Following an update to a new R version, the pipeline fails. I have traced the error to an 'assign()' call which fails. Working backwards, the first difference in variable values I get (comparing old R versus new R in parallel) is after the data read-in by ReadAffy(). In the old version, my data is summarised as:

dat <- ReadAffy(celfile.path=subdircel)  
dat  
> AffyBatch object  
> size of arrays=716x716 features (24 kb)  
> cdf=AsprgDTUa520520F (11186 affyids)  
> number of samples=27  
> number of genes=11186  
> annotation=asprgdtua520520f  
> notes=

and in the new version,

dat  
> AffyBatch object  
> size of arrays=716x716 features (15 kb)  
> cdf=AsprgDTUa520520F (11186 affyids)  
> number of samples=27  
> number of genes=11186  
> annotation=asprgdtua520520f  
> notes=

The specific bit which breaks doesn't use the whole 'dat' structure, only the 'dat@phenoData' slot. Old:

dat@phenoData
> An object of class "AnnotatedDataFrame"
>  sampleNames: 1a_N6h_ t1.CEL, 1b_N6h_t2.CEL, ..., 9c_N192h_t3.CEL  (27 total)
>  varLabels and varMetadata description:
>    sample: arbitrary numbering

and new:

> An object of class "AnnotatedDataFrame"
>  sampleNames: 1a_N6h_ t1.CEL 1b_N6h_t2.CEL ... 9c_N192h_t3.CEL (27 total)
>  varLabels: sample
>  varMetadata: labelDescription

If nothing else, there's clearly a difference in notation. And there's something which breaks my code! Is there a way to force the old structure?

Let me know if I need to be more explicit with my code. The pipeline is based on Gillespie's doi:10.1186/1756-0500-3-81

Old R-version: 2.13.2
Old affy version: 1.30.0
New R-version: 2.14.1
New affy version: 1.32.1

Thanks in advance!

Update: I think the trouble might be in how 'get' works. I use this at one stage, and comparing the outputs before and after the R-updates are quite different. Before:

get(probepackagename)  
> Object of class probetable data.frame with 121507 rows and 6 columns.

After:

> Object of class probetable data.frame with 468384 rows and 6 columns.  
> First 3 rows are:  
>                    sequence x y    Probe.Set.Name Probe.Interrogation.Position  
> 1                    <seq1> 5 1           <name1>                           13  
> 2                    <seq2> 6 1           <name2>                           13  
> 3                    <seq3> 7 1           <name3>                           13  
>   Target.Strandedness  
> 1           Antisense  
> 2           Antisense  
> 3           Antisense
bioconductor affymetrix • 2.1k views
ADD COMMENTlink modified 6.0 years ago by Biostar ♦♦ 20 • written 8.0 years ago by Bdh_Dtu20
3

This isn't the correct forum. Ask on the Bioconductor mailing list http://bioconductor.org/help/mailing-list/ and provide the output of sessionInfo() (it could be that the annotation packages have changed; are they from Bioconductor?)

ADD REPLYlink modified 3 months ago by RamRS25k • written 8.0 years ago by Martin Morgan1.6k
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