From: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Date: Thursday, 10/2/14, 12:17 AM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

> Hello Alex,
>
> It is nice to hear from you!
>
> I¹m forwarding your question to Mason Meyer and Nowlan Freese who lead
>our
> IGB support efforts.
>
> Question: Which species and genome version are you working with? Also,
> which array are you interested in?
>
> Bad news: Affymetrix is no longer supporting access to probe set
> information in IGB, but we should be able to help. Probably you remember
> IGB has a very nice visualization of probe set design sequences and
>probes
> aligned on the genomic sequence. If we can get the probe and design
> sequence information from Affymetrix, we should be able to make the probe
> set visualization available as a data set option in IGB.
>
> Mason and Nowlan - the protocol for creating the track information is not
> complex, but we ought to document how to do it in the Developer's guide
>as
> it involves multiple steps. So we should probably add this as a ³to-do²
> item (task) in IGB Jira.
>
> Alex, just to fill you in: We use a web site (nicknamed IGB Jira) to keep
> track of our ³to-do² list for IGB. If you have suggestions for new
> features to add or suggestions on how to make the user interface more
> accessible, we would love to hear them and add them to IGB Jira. The IGB
> Jira record would cite you as the source of the idea, which may be useful
> for tenure and promotion purposes. But if you prefer that we not cite
> you, that is fine, too.
>
> If you are curious, you can see what we are working on for the next
> release of IGB here: http://jira.transvar.org.
>
> I look forward to hearing from you about the array and genome you are
> working with.
>
> Thanks for reaching out,
>
> Ann

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Thursday, 10/2/14, 2:14 AM
To: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Subject: IGB Affymetrix

Hi Ann,
Thanks got getting back to me so quickly. Your help is much appreciated.
I am using a human genome and at the moment I am using data from the
human 133 Plus 2 chip set, the human 133a chip and more recently the human
gene 1.0st and HTA 2.0. Though the latter will have probe information
covering all exons etc.
Thanks again Ann- not only do I like IGB for research but I think it's a
great teaching tool for my students.
Thanks
Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Friday, 10/3/14, 12:39 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
CC: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Subject: IGB Affymetrix

Hello Alex,

My name is Mason Meyer and I'll be here to help you with whatever IGB issues you may have. We are currently working on your recent issue and I have found some sequence files that we need to resolve your issue but wanted to verify that these are the correct ones. They are:

• HG-U133 Plus 2
• HG-U133A 2
• HTA-2_0
• HuGene-1_0-st-v1.

Are these the arrays you are using? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg19, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem.

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Friday, October 3, 2014 at 1:03 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
CC: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Subject: IGB Affymetrix

Hi mason, thanks for getting in touch, yes those are the arrays I am using. In terms of the genome Annotation am not sure. I have used all of them previously (well, the first 2 at least) in different contexts. Are the sequence file of the array chips linked to genome; I thought the genome annotation file can update independently to the array chip. I might be wrong here or have the wrong end of the stick.
I hope that help.
Thanks again
Alex

Sent from my iPad

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Friday, October 3, 2014 at 3:29 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
CC: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Subject: IGB Affymetrix

Hello Alex,

Thanks for getting back to me so quickly. I thought I had the correct arrays, but just needed to double check. As far as the other question goes, it is my understanding that you need sequence files as well as an alignment file for visualization. I have located some alignment files for each array, but it looks like some of the alignment files are genome specific. I will discuss this further with the IGB team and we will continue to work to resolve your issue. I'll keep you updated on our progress.

Thanks again,

Mason Meyer

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Fri, Oct 3, 2014 at 3:44 PM
To: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Subject: Need clarification for Alex

Hey Dr. Loraine,

Sorry to bother you again, but I have briefly communicated with Alex Tonks about the Affymetrix array files. He verified that I had located the correct arrays but when asked about the genome version he was using he responded by saying that he thought the genome annotation file could update independently to the array chip. I believe I have responded to him appropriately but thought that it would be wise to run this information by you.

All of the files are now in a Dropbox link that I sent to you and all of the information in JIRA has been updated. Below I have included the link to the e-mail conversation with Alex if you want to see his exact reply.

*Link to JIRA issue with e-mail conversation:

http://204.84.7.129/browse/IGBF-210

Thanks,

Mason

From: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Date: Sat, Oct 4, 2014 at 12:41 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: Need clarification for Alex

You need to find out what version of the human genome he is working with.

In IGB’s Current Genome tab, there are menus listing available genome versions for Homo sapiens.

When you hover the mouse over one of them, you should see tooltips indicating synonyms.

Write Alex an email with the IGB name and some of the synonyms for human genome versions and ask him which one he is using. Probably he is using whatever you get when you click the Mono Lisa on the start screen, which should be the latest one. But you need to check with him first.

We can’t display the probe sets in IGB without knowing what genome assembly to use.

Also, add this email (from me) to the issue so that if this comes again, I won’t have to write all this again.

Thanks and let me know if you have any questions.

All the best,

Ann

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Mon, Oct 6, 2014 at 11:58 AM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Hello again Alex,

I did have a good weekend by the way, I hope yours was the same. I have discussed the issue of genome version with the IGB team and it turns out that we need to know the exact genome version you are using in order to display the probe sets in IGB. You may be unaware of which version you are using currently, but this info should be fairly easy to find out. In IGB, when selecting a genome, you may be clicking on the Mona Lisa icon on the start screen or you may be selecting a genome from the drop-down list on the right.

If you are selecting the Mona Lisa icon then you should be using the most recent human genome (Dec. 2013, a.k.a. hg38, etc. - see attached screenshot for additional genome name synonyms). If you are not using the Mona Lisa icon at the start of IGB then you may be selecting a genome other than the most recent genome. If so, let me know what genome you select from the drop-down box in IGB.

I hope I have explained these steps in a way that makes sense to you as I am unfamiliar with your level of IGB use. If you have any questions please let me know. Otherwise, just get back to me and let me know what buttons you click in IGB to get to the human genome so I can deduce which genome version you are using. Once we have this info we can continue to work to promptly resolve your issue.

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Mon, Oct 6, 2014 at 12:22 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Hi Mason,

Yes my weekend was pretty good. Managed to get out and not do so much work. Thanks again for your help. My IGB use is not too bad and in terms of IT I am OK. Beyond pressing buttons etc its gets a little harder. In terms of the genome version I am using it’s the hu38/ dec2013 or mona Lisa Icon.

Best wishes

Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Mon, Oct 6, 2014 at 12:25 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Thanks again Alex. This is just the info we need to continue to work on your issue. I will continue to keep you updated on our progress.

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Mon, Oct 6, 2014 at 12:27 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Thanks

On a smaller note, I removed the data access tab from the window at the bottom of the screen. I assume I can re-dock it? But I cant find the menu item to do that.

Best wishes

Alex

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Mon, Oct 6, 2014 at 12:29 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Never mind my last wuery-figured it-just close the window

Best wishes

Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Mon, Oct 6, 2014 at 1:05 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Ok, glad to hear you figured it out. If anything like that happens in the future please do not hesitate to contact me for help like you did. It is good for our team to know the things that a user may run into like that so that we know what we may need to change in IGB for the future.

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Mon, Oct 6, 2014 at 1:06 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Ok great

Best wishes

Alex

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Mon 10/27/2014 3:19 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Hi Mason,
Did you guys manage the work around on IGB-probe set annotation issue? Sorry to ask again, was not sure what the status was.

Best wishes

Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: 27 October 2014 20:43
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Hey Alex,

Sorry I have not gotten back to you yet with an update. We had hoped to resolve this issue by now but our progress was slightly delayed. My boss is going to personally take care of this issue for you so we will get back to you within the next few days if all goes well. I apologize if we have inconvenienced you in any way.

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Mon 10/27/2014 4:54 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Thanks for the update, not at all inconvienienced, just happy to get some help . Thanks for everything

Best wishes

Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: 28 October 2014 15:16
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Hey Alex,

We are working on your issue but it seems like we may have to go about it a different way than planned. Many of the necessary files are no longer available on the Affymetrix site so we are currently writing some code to resolve the issue a different way.

If you are able to would you please send me the GPL I.D. of your highest priority arrays?

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Tue 10/28/2014 11:58 AM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Hi Mason,
Many thanks,
Whats GPL I.D?

Alex

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Tue 10/28/2014 12:10 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

If you mean GeneChip type:-
GeneChip® Human Genome U133 Plus 2.0 Array
GeneChip® Human Transcriptome Array 2.0

But I don’t know the GPL sorry?
bw
Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Tue 10/28/2014 12:10 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Hey Alex,
The GPL I.D. is an external accession I.D. used to reference the array to other databases. I believe the GPL I.D. for [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array is "GPL570" and the GPL I.D. for [HG-U133A] Affymetrix Human Genome U133A Array is "GPL96". My boss just wanted me to verify these I.D.s before continuing to resolve the issue. I have looked online and am very confident that these are the correct GPL I.D.s for these arrays. If you have any additional information to give me please let me know. I will get back to you soon with a status update.
Thanks again,
Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Tue 10/28/2014 12:14 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

Hi Mason yes this was the conclusion I was reaching as I was searching google.
GPL17585 and GPL17586 - was for Affymetrix Human Transcriptome Array 2.0

thanks
Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Tue 10/28/2014 12:18 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Ok thanks Alex. And just to make sure, you previously told me that HG-U133 Plus 2 and HG-U133A were your main priorities. Is still the case?
Thanks,
Mason

From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Tue 10/28/2014 12:19 PM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: IGB Affymetrix

The Plus 2 is the main one, yes. Not so much 133A.
thanks
Alex

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Wed 10/29/2014 3:04 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix

Alright, thanks again for the info Alex. I will keep you updated on the progress. We hope to have this issue resolved by the end of the week.

Thanks again,
Mason

From: Alex Tonks <TonksA@cardiff.ac.uk>
Sent: Wednesday, October 29, 2014 3:55 PM
To: Mason Meyer <mason.meyer@my.lr.edu>
Subject: RE: IGB Affymetrix Issue

Excellent thanks

Best wishes

Alex

From: Mason Meyer <mason.meyer@my.lr.edu>
Sent: Mon 11/3/2014 7:17 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: RE: IGB Affymetrix Issue

Hey Alex,

Sorry again for the delay on resolving your issue. My boss has put together a file for you that is available here:

https://bitbucket.org/lorainelab/affyprobesetsforigb/downloads

Open the file “GPL570.HG-U133_Plus_2.link.psl” into IGB (you can drag and drop right into IGB after selecting Homo sapien as your genome). When doing this, make sure the file with the .tbi extension is in the same directory as the the link.psl file.

My boss told me to include a few tips for you as well. You may want to configure the annotation file to display the ID field as the label field. Also, remember that you can combine the plus and minus strands if desired.

We wanted to send you this file so that you could use it now for your purposes but my boss is currently working on adding it to the IGB Quickload site as well, so in the future look for similar data files under the Affymetrix folder under the Data Access panel in IGB. Please let us know if anything seems odd or if you need help in displaying this file in IGB properly. Let us know how it works for you!

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Sent: Tue 11/4/2014 4:09 PM
To: Mason Meyer <mason.meyer@my.lr.edu>
Subject: RE: IGB Affymetrix Issue

Hi Mason,
Many thanks to yourself, your lab colleagues and Loraine. Your instructions were great and easy to implement. However the handy tip about ID display was the best!.

Thanks again-it works great and I am very appreciative.
Best wishes

Alex

From: Mason Meyer <mason.meyer@my.lr.edu>
Sent: Wed 11/5/2014 5:50 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: RE: IGB Affymetrix Issue

Hey Alex,

I hope the files that the team made for you are still suiting your needs. Ann (my boss) wanted me to get back in touch with you to let you know that when opening the file into IGB, you should probably use the “GPL570.HG-U133_Plus_2.link.psl.gz” file, which conatins the .GZ extension, as this will load faster. We’re very glad we had the opportunity to help you out. Please let us know if there is anything else we can do for you or any recommendations you may have that may help IGB evolve in the future.

Thanks again,

Mason Meyer

From: Alex Tonks <TonksA@cardiff.ac.uk>
Sent: Thu 11/6/2014 2:35 AM
To: Mason Meyer <mason.meyer@my.lr.edu>
Subject: RE: IGB Affymetrix Issue

Hi Mason,
Thanks again and please pass on my thanks to Ann.

Best wishes