[BioC] chipAlongChrom problem in Ringo

Joern Toedling toedling at ebi.ac.uk
Fri Jan 23 10:50:14 CET 2009


this seems to be the source of the problem. The identifiers of the
probes that you remapped are of this form
while in the ExpressionSet they are of the form
Were both these types of identifiers given in your array description
file (ndf)? If so, and if there's a one-to-one mapping between these,
you can probably use these as well as featureNames in the ExpressionSet.
You will have to look into the raw RGList type data and see if these
identifiers of the type 5313_0084_0040 are also in there. Have a look at
If so you can set these identifiers to also be the featureNames of the
ExpressionSet by changing the argument "idColumn" of the function
preprocess to this column header.
Otherwise, if the identifiers of this type 5313_0084_0040 are not
unique, you might at the moment lose information from your data, as only
uniquely mapped probes are considered for finding enriched regions. In
this case, you will probably have to assign the correct unique
identifiers to the probe sequences in your Fasta files and you might
have to run Exonerate again in this case.
Hope this helps.


Jianping Jin wrote:
>> str(probeAnno["5.index"])
> chr [1:21152] "5313_0084_0040" "5313_0760_0290" "5313_0060_0330" ...
>> featureNames(X)[1:30]
> [1] "CHR10FS100018407" "CHR10FS100018507" "CHR10FS100018612"
> "CHR10FS100018717"
> [5] "CHR10FS100018817" "CHR10FS100018927" "CHR10FS100019007"
> "CHR10FS100019103"
> [9] "CHR10FS100019228" "CHR10FS100019328" "CHR10FS100019428"
> "CHR10FS100019503"
> [13] "CHR10FS100019603" "CHR10FS100019703" "CHR10FS100019824"
> "CHR10FS100019927"
> [17] "CHR10FS100020027" "CHR10FS100020117" "CHR10FS010119532"
> "CHR10FS010119652"
> [21] "CHR10FS010119737" "CHR10FS010119840" "CHR10FS010119947"
> "CHR10FS010120052"
> [25] "CHR10FS010120142" "CHR10FS010120232" "CHR10FS010120343"
> "CHR10FS010120453"
> [29] "CHR10FS010120552" "CHR10FS010120652"

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