This is just let anyone who was following the thread regarding missing probes the illumina v3 annotation packages that there are no missing probes (as far as we know). See below. Lynn Amon -------- Original Message -------- Subject: RE: SFC#00027211 Response from SWITCHTOI: Contact Us Date: Mon, 2 Jun 2008 11:20:59 -0700 From: TechSupport-ILMN <techsupport-ilmn@illumina.com> To: Lynn Amon <lamon at="" fhcrc.org=""> CC: Baker, Shawn <scbaker at="" illumina.com="">, <atarca at="" med.wayne.edu=""> References: <20083005.204012.4f7ab832 at fhcrc.org> <66E8F8C886F7E84081753337F24F0EFE2D9C71 at ilmn-mail03.illumina.com> <48408FB7.7090204 at fhcrc.org> Hi Lynn, Thank you for the clarification. We have discovered that the .bgx manifest being used in the case you mention was actually a beta version. In the released version, these 5 probes are not included. You will find both the released .bgx and its corresponding readable .txt version on the switchtoi website I mentioned. (http://www.switchtoi.com/annotationfiles.ilmn) I do apologize for any confusion this may have caused. Please don't hesitate to contact us with any additional questions. Best regards, elizabeth ______________________________ Elizabeth Boyer Scientific & Technical Support Illumina, Inc 9885 Towne Centre Drive San Diego, CA 92121 (800) 809-4566 (858) 202-4804 fax E-mail: TechSupport at illumina.com Web: www.illumina.com This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. -----Original Message----- From: Lynn Amon [mailto:lamon@fhcrc.org] Sent: Friday, May 30, 2008 4:37 PM To: TechSupport-ILMN Cc: Baker, Shawn; cbrady at illumina.com; atarca at med.wayne.edu Subject: Re: SFC#00027211 Response from SWITCHTOI: Contact Us Hello Elizabeth, Thank you for responding. I do not have the appropriate software to read a bgx file but I was going on an exchange with a scientist (CC'd) via the Bioconductor mailing list who said he has a bgx file with those five probes. I've attached that email exchange. Thanks again, Lynn TechSupport-ILMN wrote: > Hi Lynn, > > Thank you for contacting Illumina technical support. I'm afraid I am > unable to replicate what you have reported. I have searched both the > .bgx file and .txt version found on our www.switchtoi.com website > (http://www.switchtoi.com/annotationfiles.ilmn) and did not find the 5 > probes you mentioned in either file. Could you tell me where you > downloaded the .bgx manifest you are using? I want to be sure we are > using the same files. > > Best regards, > elizabeth > > ______________________________ > Elizabeth Boyer > Scientific & Technical Support > Illumina, Inc > 9885 Towne Centre Drive > San Diego, CA 92121 > > (800) 809-4566 > (858) 202-4804 fax > E-mail: TechSupport at illumina.com > Web: www.illumina.com > > > -----Original Message----- > From: Lynn Amon [mailto:lamon at fhcrc.org] > Sent: Friday, May 30, 2008 1:40 PM > To: TechSupport-ILMN; scbaker at illumina.com; cbrady at illumina.com > Subject: SFC#00027211 Response from SWITCHTOI: Contact Us > > FirstName: Lynn > LastName: Amon > Title: Staff Scientist > Organization: Fred Hutchinson Cancer Research Center > Email: lamon at fhcrc.org > Phone: 206-667-7836 > Comments: Why are there probes in the HumanV3 bgx files that missing > from the corresponding txt files? In the Ref8 arrays, there are five > missing (probeIDs): > 2230095 290491 450670 5360291 6250095 > Thank you, > Lynn Amon > Fred Hutchinson Cancer Research Center > >