[BioC] Ringo/Starr getProfiles function

[Noah Dowell]

Hello All,


Another problem has come up that hopefully someone can provide some assistance with...

I am trying to plot ChIP data in relation to the TSS as show in the Starr vignette but the following error comes up when I call the getProfiles function:

> profile = getProfiles(wtNucRatio, probeAnnot, tssAnno, 800, 800, feature = "TSS", borderNames = "TSS", method = "basewise")
chromosome NA  Error in probeAnno[paste(chr[i], "index", sep = ".")] : 
 No mapping 'NA.index' in this 'probeAnno' object.





My particular probeAnno object (probeAnnot) was created using both functions recommended on this board and in the vignette.  For example:


using the Ringo function of:    posToProbeAnno

> probeAnnot <- posToProbeAnno(pos, genome="Saccer", microarrayPlatform = "Affymetrix")

or the Starr function of bpmapToProbeAnno

> probeAnno = bpmapToProbeAnno(bpmap)

both methods print out the probeAnno mapping for chromosome and do not throw any errors so I assumed the object was made correctly.


So I think the error above may be coming from elsewhere but I cannot find it and do not know how to fix it.  Any help would be greatly appreciated.

PS.  I created the tssAnno using biomaRt and everything in that looks to be okay...

noah