ok ... thank you for the link and the explanation. I was assuming it's opened to everyone, as any other control probes. But yes, it's their right. I understand. Again many thanks. With kind regards, Ema ________________________________ From: "Tim Triche, Jr." <tim.triche@gmail.com> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Wednesday, August 28, 2013 9:42 PM Subject: Re: [BioC] minfi: control probes sequence One could, in theory, reverse engineer the probes, but that could be rather troublesome and it's hard to believe it would be worthwhile. One issue is that many of the control probes aren't actually supposed to bind to anything, so there's no particular reason to use a particular base or bases.  The ones that are supposed to bind to a particular reaction product are documented by Illumina: http://supportres.illumina.com/documents/myillumina/90666eaa-0c66-48b4 -8199-3be99b2b3ef9/genomestudio_methylation_v1.8_user_guide_11319130_b .pdf (beginning on page 63) But, again, there's no disclosure of the actual control probe sequences.  My recollection (having asked in the past) is that the sequences are considered proprietary, presumably because Illumina spent time/money optimizing them. HTH, --t On Wed, Aug 28, 2013 at 12:36 PM, Tim Triche, Jr. <tim.triche@gmail.com> wrote: Ask Illumina. > > > > > wrote: > > >> >>ok... >>Is there any possibility or how to get the information about it? >>Many thanks. >> >> >>With kind regards, >>Ema >> >> >> >> >> >>________________________________ >> From: "Tim Triche, Jr." <tim.triche@gmail.com> >>Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> >>Sent: Wednesday, August 28, 2013 9:02 PM >>Subject: Re: [BioC] minfi: control probes sequence >> >> >> >>Illumina does not disclose the control probe sequences >> >> >> >> >> >> >> wrote: >> >> >>> >>>Dear All, >>> >>>(This is a cross posting message) >>>recently, I played with minfi package, just copy-pasted the vignette, to make me familiar how to analyse the Illumina HM 450k data with it. >>>I stumbled a cross by not knowing how to retrieve the control probes sequences in it. >>>I guessed, it is related to the annotation. >>>I have searched from the archives and tried but still no success. >>> >>>Any help, is really appreciated. >>>Thank you very much in advance. >>> >>>With kind regards, >>>Ema >>>        [[alternative HTML version deleted]] >>> >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor@r-project.org >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> >> >>-- >> >>He that would live in peace and at ease, >>Must not speak all he knows, nor judge all he sees. >> >> >> >>Benjamin Franklin, Poor Richard's Almanack >> >> > > > >-- > >He that would live in peace and at ease, >Must not speak all he knows, nor judge all he sees. > > > >Benjamin Franklin, Poor Richard's Almanack -- He that would live in peace and at ease, Must not speak all he knows, nor judge all he sees. Benjamin Franklin, Poor Richard's Almanack [[alternative HTML version deleted]]