Hi, I am following the 'Analysis of Bead-level Data using beadarray' from beadarray bioconductor page. I am at the controlProbe step and it seems like the data(controlProfile) command brings up information for a very old version of beadArray (only 76 control probes). I was wondering where I could get the PROBE_IDs for the newer control probes especially for platforms HuRef8v3 and HumanHT12v4. Do PROBE_IDs change between v3 and v4? Lastly, is there a place to find the 'Reference Manuals' in TeX instead of pdf? I ask because sometimes parameters are cut off and also would make things easier to grep. Thanks, Ying Wu [[alternative HTML version deleted]]

Hi, Control information for current expression platforms is stored in the ExpressionControlData object in beadarray. >data(ExpressionControlData) > names(ExpressionControlData) [1] "Humanv3" "Humanv2" "Humanv1" "Mousev2" "Mousev1" "Mousev1p1" [7] "Ratv1" "Humanv4" > head(ExpressionControlData[["Humanv3"]]) Array_Address Reporter_Group_Name Reporter_Group_Identifier 1 4730189 negative permuted_negative 2 5700037 negative permuted_negative ... The controlProfile object is specifically for the example dataset supplied with the package (it is indeed a very old dataset). It is also example of how users with data other than the standard platforms listed in ExpressionControlData can use the functions in the pacakge. If you have set the annotation of the beadLevelData object when you use readIllumina, or later with setAnnotation, then this control information should be available to the plotting and summarisation functions. Hope this helps, Mark On Wed, Nov 3, 2010 at 10:02 PM, Ying W <daiyingw at="" gmail.com=""> wrote: > Hi, > I am following the 'Analysis of Bead-level Data using beadarray' from > beadarray bioconductor page. > > I am at the controlProbe step and it seems like the data(controlProfile) > command brings up information for a very old version of beadArray (only 76 > control probes). > I was wondering where I could get the PROBE_IDs for the newer control probes > especially for platforms HuRef8v3 and HumanHT12v4. > Do PROBE_IDs change between v3 and v4? > Lastly, is there a place to find the 'Reference Manuals' in TeX instead of > pdf? I ask because sometimes parameters are cut off and also would make > things easier to grep. > > Thanks, > Ying Wu > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >