[BioC] Error using ABarray

[Martin Morgan]

Hi Ingrid -- I think 

> Error in is.null(x) || all.equal(x, y, check.attr = FALSE) : 
>   invalid 'y' type in 'x || y'

is coming from Biobase, where it is trying to combine data.frame's,
probably from phenoData objects. Probably there is a name mismatch
between the sample names identified in the dataFile and designFile
arguments.

In general traceback() after the error occurs can give some insight
into the nature of the problem; in this case the error is quite
obscure and deeply nested, so this might not have been that helpful.

An updated version of Biobase should be available via biocLite in a
little more than 24 hours time; I made this change earlier, but
neglected to commit it to the release branch.

Martin


Ingrid H. G. Østensen <Ingrid.H.G.Ostensen at rr-research.no> writes:

> Hi
>
> I have got an error when I am using ABarray:
>
>> eset=ABarray("data.txt", "Heidi_desing.txt", "sampleOrigin") 
> Using arrayName to match experiment with signal in file: data.txt 
> The sample names are:
> [1] "1" "2" "3" "4" "5" "6"
> AssayNames in dataFile: data.txt 
>  [1] "HA004J2_1A_1" "HA004J7_1A_2" "HA004JB_1A_3" "HA004JD_1B_1" "HA004JI_1B_2" "HA004JK_1B_3" "HA004JN_2A_1" "HA004JO_2A_2" "HA004JP_2A_3" "HA004JS_2B_1" "HA004JT_2B_2" "HA004JU_2B_3"
>
> The following arrays were excluded from analysis:
> [1] "HA004JN_2A_1" "HA004JO_2A_2" "HA004JP_2A_3" "HA004JS_2B_1" "HA004JT_2B_2" "HA004JU_2B_3"
> Reading data from data.txt ......
>     This may take several minutes....
> Finished data reading.
> The results will be in the folder: Result_sampleOrigin/ 
> [1] "Creating plot for Signal Hybridization_Control ..."
> [1] "Creating plot for Signal Negative_Control ..."
> [1] "Creating plot for Signal IVT_Kit_Control_BIOB ..."
> [1] "Creating plot for Signal IVT_Kit_Control_BIOC ..."
> [1] "Creating plot for Signal IVT_Kit_Control_BIOD ..."
> [1] "Creating plot for Signal RT_Kit_Control_DAP ..."
> [1] "Creating plot for Signal RT_Kit_Control_LYS ..."
> [1] "Creating plot for Signal RT_Kit_Control_PHE ..."
>
> Perform basic analysis for non-normalized data ...
> [1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3"
> Error in is.null(x) || all.equal(x, y, check.attr = FALSE) : 
>   invalid 'y' type in 'x || y'
>
>
>
>
> I have seen that others have had the same error but could not find a reply to that e-mail. Does any one know what might be wrong? (I also get the same error using R 2.5.1)
>
>
> R version 2.6.0 (2007-10-03) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
>  [1] tcltk     splines   tools     stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] ABarray_1.6.0   multtest_1.18.0 survival_2.34   Biobase_1.16.1 
>
>
> Regards,
> Ingrid
>
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793