RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays
Hi, You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix: http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip Regards, Guido From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon Sent: Wednesday, February 20, 2013 09:06 To: aroma-affymetrix@googlegroups.com Subject: [aroma.affymetrix] Re: Gene 2.0 ST arrays Hello all, It may be a little out of the current thread discussion, but i want to test a dataset which uses HuGene-1_0-st and HuGene-2_0-st arrays for my analysis tool in geneXplain platform. I am getting lot of datasets using HuGene-1_0-st in GEO but not HuGene-2_0-st. Can anyone help me with this. How should i get publicly available dataset using this platform. Is it also denoted by some other name. Any pointers in this regard is really appreciated. Thanks and Regards, Neetu On Thursday, 6 December 2012 19:24:58 UTC+5:30, Maria Traka wrote: Hi guys, probably you've already given the answer somewhere but can i use aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)? Presumably the same way as 1.0 arrays? Thanks in advance, Maria -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.commailto:aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.commailto:aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
Re: [aroma.affymetrix] Re: Gene 2.0 ST arrays
Thanks Guido. but the site says ' Sample data is no longer provided in individual files or in .CAB file format, and is thus not compatible with Microarray Suite (MAS) or with versions of GCOS that do not have DTT version 1.1 or higher installed. I will have to install many things to check if it is working properly. I would prefer if i get a dataset listed in GEO or ArrayExpress for testing my analysis method. Is it possible that none of the publicly available datasets use this platform? Thanks and Regards, Neetu On Wed, Feb 20, 2013 at 2:29 PM, Hooiveld, Guido guido.hooiv...@wur.nlwrote: Hi, You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix: http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip ** ** Regards, Guido ** ** *From:* aroma-affymetrix@googlegroups.com [mailto: aroma-affymetrix@googlegroups.com] *On Behalf Of *Neetu Tandon *Sent:* Wednesday, February 20, 2013 09:06 *To:* aroma-affymetrix@googlegroups.com *Subject:* [aroma.affymetrix] Re: Gene 2.0 ST arrays ** ** Hello all, It may be a little out of the current thread discussion, but i want to test a dataset which uses HuGene-1_0-st and HuGene-2_0-st arrays for my analysis tool in geneXplain platform. I am getting lot of datasets using HuGene-1_0-st in GEO but not HuGene-2_0-st. Can anyone help me with this. How should i get publicly available dataset using this platform. Is it also denoted by some other name. Any pointers in this regard is really appreciated. ** ** Thanks and Regards, Neetu On Thursday, 6 December 2012 19:24:58 UTC+5:30, Maria Traka wrote: Hi guys, probably you've already given the answer somewhere but can i use aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)? Presumably the same way as 1.0 arrays? Thanks in advance, Maria -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays
Hi Neetu, I don't fully understand. I just re-downloaded the file through the link I mentioned before, and obtained a ZIP of 532MB. This ZIP contains 24 HuGene 2.0 CEL files. Moreover, 24 HuGene 2.1 CEL files are included as well. Indeed, I also concluded that yet no ST2.0 arrays are available through GEO. You have to realize that these 2.0 arrays are only on the market for less than a year or so, and it takes some time for labs to start using these chips, let alone to publish data that was generated. And it is only at that moment that submitting data to GEO or ArrayExpress is required. Regards, Guido From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon Sent: Wednesday, February 20, 2013 11:37 To: aroma-affymetrix@googlegroups.com Subject: Re: [aroma.affymetrix] Re: Gene 2.0 ST arrays Thanks Guido. but the site says ' Sample data is no longer provided in individual files or in .CAB file format, and is thus not compatible with Microarray Suite (MAS) or with versions of GCOS that do not have DTT version 1.1 or higher installed. I will have to install many things to check if it is working properly. I would prefer if i get a dataset listed in GEO or ArrayExpress for testing my analysis method. Is it possible that none of the publicly available datasets use this platform? Thanks and Regards, Neetu On Wed, Feb 20, 2013 at 2:29 PM, Hooiveld, Guido guido.hooiv...@wur.nlmailto:guido.hooiv...@wur.nl wrote: Hi, You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix: http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip Regards, Guido From: aroma-affymetrix@googlegroups.commailto:aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.commailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon Sent: Wednesday, February 20, 2013 09:06 To: aroma-affymetrix@googlegroups.commailto:aroma-affymetrix@googlegroups.com Subject: [aroma.affymetrix] Re: Gene 2.0 ST arrays Hello all, It may be a little out of the current thread discussion, but i want to test a dataset which uses HuGene-1_0-st and HuGene-2_0-st arrays for my analysis tool in geneXplain platform. I am getting lot of datasets using HuGene-1_0-st in GEO but not HuGene-2_0-st. Can anyone help me with this. How should i get publicly available dataset using this platform. Is it also denoted by some other name. Any pointers in this regard is really appreciated. Thanks and Regards, Neetu On Thursday, 6 December 2012 19:24:58 UTC+5:30, Maria Traka wrote: Hi guys, probably you've already given the answer somewhere but can i use aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)? Presumably the same way as 1.0 arrays? Thanks in advance, Maria -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.commailto:aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.commailto:aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.commailto:aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.commailto:aroma-affymetrix%2bunsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix
Re: [aroma.affymetrix] Re: Gene 2.0 ST arrays
Thanks Guido, Your reply is very helpful. I will download and check. You are right it is too early to expect labs using these chips. Best regards, Neetu On Wed, Feb 20, 2013 at 4:26 PM, Hooiveld, Guido guido.hooiv...@wur.nlwrote: Hi Neetu, I don’t fully understand. I just re-downloaded the file through the link I mentioned before, and obtained a ZIP of 532MB. This ZIP contains 24 HuGene 2.0 CEL files. Moreover, 24 HuGene 2.1 CEL files are included as well. Indeed, I also concluded that yet no ST2.0 arrays are available through GEO. You have to realize that these 2.0 arrays are only on the market for less than a year or so, and it takes some time for labs to start using these chips, let alone to publish data that was generated. And it is only at that moment that submitting data to GEO or ArrayExpress is required. ** ** ** ** Regards, Guido ** ** *From:* aroma-affymetrix@googlegroups.com [mailto: aroma-affymetrix@googlegroups.com] *On Behalf Of *Neetu Tandon *Sent:* Wednesday, February 20, 2013 11:37 *To:* aroma-affymetrix@googlegroups.com *Subject:* Re: [aroma.affymetrix] Re: Gene 2.0 ST arrays ** ** Thanks Guido. but the site says ' Sample data is no longer provided in individual files or in .CAB file format, and is thus not compatible with Microarray Suite (MAS) or with versions of GCOS that do not have DTT version 1.1 or higher installed. ** ** I will have to install many things to check if it is working properly. I would prefer if i get a dataset listed in GEO or ArrayExpress for testing my analysis method. Is it possible that none of the publicly available datasets use this platform? ** ** Thanks and Regards, Neetu On Wed, Feb 20, 2013 at 2:29 PM, Hooiveld, Guido guido.hooiv...@wur.nl wrote: Hi, You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix: http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip Regards, Guido *From:* aroma-affymetrix@googlegroups.com [mailto: aroma-affymetrix@googlegroups.com] *On Behalf Of *Neetu Tandon *Sent:* Wednesday, February 20, 2013 09:06 *To:* aroma-affymetrix@googlegroups.com *Subject:* [aroma.affymetrix] Re: Gene 2.0 ST arrays Hello all, It may be a little out of the current thread discussion, but i want to test a dataset which uses HuGene-1_0-st and HuGene-2_0-st arrays for my analysis tool in geneXplain platform. I am getting lot of datasets using HuGene-1_0-st in GEO but not HuGene-2_0-st. Can anyone help me with this. How should i get publicly available dataset using this platform. Is it also denoted by some other name. Any pointers in this regard is really appreciated. Thanks and Regards, Neetu On Thursday, 6 December 2012 19:24:58 UTC+5:30, Maria Traka wrote: Hi guys, probably you've already given the answer somewhere but can i use aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)? Presumably the same way as 1.0 arrays? Thanks in advance, Maria -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. ** ** -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post
