Affy to Illumina conversions complete?

[Ann Turner]

father/mother/child trios

I'd be interested in comparing match lists for father/mother/child trios who have data for both the Affy and Illumina chips. Be sure to set your Matches to All before downloading the CSV files. My e-mail address is [email protected].

[AngeliaR]

FB response on "Affy"

Question posted to Facebook:
Is it true that Family Finder "Affy" results will be removed without notification of when this will happen so people can save them?

I don't think people are really informed about whether the old results will simply disappear or if they will be maintained for a short period of time.

Comment from Matt Dexter:
FTDNA has placed a small message on the FF Affy Matches page - at the top. It's lost in the jungle of so much other text though... I doubt many people won't notice it there.

Answer from FTDNA on Facebook:
Back in February, when we announced the conversion and sent a letter to all our customers we explained all details related to the conversion and we provide a link to an FAQ section where we included a date for removing the Affy results, which are now totally irrelevant: http://www.familytreedna.com/faq/ans....aspx?faqid=39

As a courtesy, we now included a first paragraph in the Affy results page confirming what we informed earlier.
___________________________

So, now we have it. Those of us who read the forum or facebook notices know that FTDNA has communicated this information. Hopefully, most of the people actively working with Affy match data has seen the postings and updates...
___________________________

Since we have been encouraged to migrate toward FB, I thought I would see what happens when questions like this are posed in that arena. Pretty quick response, with links. :-)


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[rewarren]

Large Affy>Illumina match losses

For the two kits that I monitor that were tested on both chips, I found 83% losses of matches from Affy to Illumina on one and 75% losses on the other.
Most of the lost matches were 5th-Distant, but there were also a few 4th-Distant cousins.

For those matches that appeared in both lists, almost half were the same relationship level. All but one of the others showed a closer relationship.

In addition to different samples, are the criteria for the new Illumina chip matches higher?

[mkdexter]

Question posted to Facebook:
Is it true that Family Finder "Affy" results will be removed without notification of when this will happen so people can save them?

I don't think people are really informed about whether the old results will simply disappear or if they will be maintained for a short period of time.

Comment from Matt Dexter:
FTDNA has placed a small message on the FF Affy Matches page - at the top. It's lost in the jungle of so much other text though... I doubt many people won't notice it there.

Answer from FTDNA on Facebook:
Back in February, when we announced the conversion and sent a letter to all our customers we explained all details related to the conversion and we provide a link to an FAQ section where we included a date for removing the Affy results, which are now totally irrelevant: http://www.familytreedna.com/faq/ans....aspx?faqid=39

As a courtesy, we now included a first paragraph in the Affy results page confirming what we informed earlier.
___________________________

So, now we have it. Those of us who read the forum or facebook notices know that FTDNA has communicated this information. Hopefully, most of the people actively working with Affy match data has seen the postings and updates...
___________________________

Since we have been encouraged to migrate toward FB, I thought I would see what happens when questions like this are posed in that arena. Pretty quick response, with links. :-)


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Ooops.. I actually meant to say I doubt people will... not won't... notice it there.. in other words its hard to find.

[mkdexter]

In addition to different samples, are the criteria for the new Illumina chip matches higher?

Hard to say at this point because they have made multiple adjustments to the algorithm. Good question!

[AngeliaR]

Let the chips fall...

I understood that it was very difficult to see the Affy if you weren't specifically looking for it. (I don't have Affy results myself, but do get the confusion and frustration over this issue.) Kind of goes along with the general theme we've seen developing. It's a positive concession that there was a posting of anything anywhere. It still feels like an uphill battle on the communication front... so, when the Affy results do go away, and people were not aware of it, let the chips fall where they may. There has been ample discussion of what this means to people and their genealogy research efforts.

Communication kind of goes beyond mere "courtesy" and extends into effective business operation. FTDNA has the best technical services currently in the genealogy dna market, bar none; but, it would be nice if the "softer" support services were seen as just as necessary to the overall mission and customer satisfaction.

I remain a solid FTDNA fan, but am not beyond exploring other options and being aware of developments elsewhere too.


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[barbara]

AngeliaR, very nicely said. As for myself, I'm pissed. I did not understand that I needed to be a computer tech to read my FF results. I have not read my Affy or Illuminia raw data.
Now I am pressured/forced to receive FTdna notifications/information from facebook that I have chose not to join; not from the company I have tested with 3 times since 2003, that has my DNA in storage for 25 years. Insane... If you were to read the FF forum over this pass year, you may wonder what planet is this. I stay confused..

[dwight]

One thing I don't understand is - what's the rush? What is the cost to FTDNA of just leaving the Affy results on their for awhile longer? A little bit of server space and time, true. It's not like have to do anything with them - just leave them there for people to access. I have no idea what % of their customer base reads this forum as often as even once a month, but i'd be amazed if it's over 25%. Admittedly I know nothing about any of what lies behind their actual decision making process on this, and there quite likely are factors that to them are important but wouldn't even be thought of by those of us outside the industry... Nevertheless, I would think the risk of pissing off paid customers who missed the import of a single email sent in February, but come back in June or August and find the data they knew and were familiar with to be no gone, longer in existence, would be a risk worthy of some effort to avoid. But this is just me, and since I can't seem to stay away from the forum for more than 30 minutes at a time, this is obviously not my problem!

AngeliaR, very nicely said. As for myself, I'm pissed. I did not understand that I needed to be a computer tech to read my FF results. I have not read my Affy or Illuminia raw data.
Now I am pressured/forced to receive FTdna notifications/information from facebook that I have chose not to join; not from the company I have tested with 3 times since 2003, that has my DNA in storage for 25 years. Insane... If you were to read the FF forum over this pass year, you may wonder what planet is this. I stay confused..

[mkdexter]

I think very few of all their customers read this forum, even less read other forums and I think the majority of the FTDNA customer base does not read Face Book posts. Those are just my opinions and I might be wrong but that's what I think.

This morning I had a phone discussion with FTDNA about the Affy concerns, questions and posts here. I even forwarded a few posts and emails I have received their way.

From what I gathered in my discussion this morning, from FTNDA's point of view it is a supporting Affy issue. They can't support Affy anymore and have moved to a new platform. They want to focus on Illumina and supporting it. They told me having the Affy matches listed may lead to questions they can no longer research or support.

From what I see (my opinion here) as the customer perspective is that we want to know why we've lost around 50% FF speculative Affy matches. Are Affy still considered past matches? Did we lose Affy matches because the platforms test different SNPs? Did we lose Affy matches because the Illumina algorithm has tighter tolerances? What is the reasoning behind removing the Affy lists next week?

It seems FTDNA would want to provide an official explanation and answer to these and other questions and communicate some of the behind their scenes reasoning. That answer is in the hands of Max and Bennett as to if they will or not. We will see what transpires over the course of the next few days.

I said: "Get ready for the phone calls."

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[k.o.gran]

Thanks for doing that Matt! If only FTDNA would hire you as a "community manager".

[CAM]

Matches

Matt,
Thank you for passing info. to FTDNA . You are right they will be hearing it.

Total Affy Matches 77
Affy matches I did not get with Illumina 52
Affy convertd to Illumina 25

My father did not get any of the matches I lost due to the conversion and I am surprised with this.

My mothers brother got 4 of the matches I lost due to the conversion. One of his matches I did not get is Junior but we both got his father.

Better Luck in my next life I guess I will have to wait to see.
Cheryl

[nathanm]

From what I see (my opinion here) as the customer perspective is that we want to know why we've lost around 50% FF speculative Affy matches. Are Affy still considered past matches? Did we lose Affy matches because the platforms test different SNPs? Did we lose Affy matches because the Illumina algorithm has tighter tolerances?

I didn't test on Affy, so it's not an issue for me personally. But I'd guess the answer to your last two questions I quoted is yes.

I wonder how much effect this actually has on peoples' matches, at least ones with a reasonable expectation of finding a paper trail to a common ancestor. Did many people lose matches they'd already figured out how they're related? If so, maybe they're showing up as sharing some DNA, but not quite meeting the match threshold for the Illumina chip. I wonder if FTDNA could somehow make exceptions to the criteria, and allow lower resolution matches to show up when they're already known relationships? It wouldn't hurt to ask.

More generally, I agree with the sentiment FTDNA needs to work on their customer service. Just being a little more proactive and explaining changes better could go a long way to maintaining customer goodwill.

[AngeliaR]

Feedback

My suggestion would be to give direct feedback, starting now since we have been given some pretty clear responses... email the contact numbers given as a start, call reps, etc...

But, there could be some power in the use of social media to let concerns be known. Afterall, there are 10,000+ "likes" in the mix and a certain degree of public awareness/pressure to respond in an appropriately sensitive and thoughtful manner. This could impact potential future customers as well as existing ones who may not know about the bumps that have been experienced as a part of the transition. Maybe now is the time to use FB for something other than a "like" count and state the issue publicly.

The beauty of that last option is that we have been encouraged to use it by FTDNA themselves... as their chosen means of communication with us.
__________________________

The upgrade and free testing to existing Affy customers to convert to the new platform should have been a HUGE positive PR move. It had the potential power to create enthusiastic supporters and good will going forward indefinitely... So, what happened? Why are people STILL grumbling about a free upgrade?

What analysis was done on what the customers wanted/needed/expected from the move? How was it communicated? Even now, how do the customers FEEL about the changes being made?

When you put a lot of work and personal effort into a project like family research, you want to know it's going somewhere. This loss of data without any official recognition or explanation FEELS somewhat like a betrayal of trust.



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[Geneadict]

Alex Khomenko, a 23andMe software engineer who just left 23andMe, announced last Nov 2010 that they had 60,000 customers. I think newer numbers have been estimates from customers. I don't believe there's a way to see how many of the 60,000 are just there for the medical test but its a significant number of them.

I estimate FTDNA is at 9500 FF tests. I have not asked them because I don't really care anymore. Paul usually does his homework though.

The database growth is more important once you're in the system. It used to be 1000 a month give or take for both companies but its higher now and it fluctuates depending on sale periods etc.

Same source, noted 75,000 as of Feb 2011 in these articles (which were posted in a 23andMe community thread by Glenn Nolen)

http://www.genomesunzipped.org/2011/...s.php#comments

http://www.quora.com/How-many-paying...s-23andMe-have

Based on new matches, 23andMe has also clearly had higher ongoing growth rate since December 2010 as of result of lower pricing and various sales thus the reason for my earlier estimate of 80-90k.

(also, 50k threshold was announced late June 2010)

http://spittoon.23andme.com/2010/06/22/23andme-and-a-new-paradigm-for-research/

On the FTDNA side, my estimates may still be on the high end. I originally thought FF was close to the 10k mark last summer after their "Bull Rush" BETA orders and public launch and comparing match ratios to 23andMe's Relative Finder (RF). However, Matt set me straight and it turned out that my Affy match ratios were nearly double that of my father-in-laws and others and thus part of my large match loss on FFs Illumina.

Of course both numbers are moving and you may get different answers depending on who you ask and whether you are talking about kits issued/sold versus results in the database (as there would be a lag) and in the case of 23andme would also be a small percent that have opted out of RF included in the totals.

Of course for 23andMe there are the issues with low response rate and health vs genealogy interest that have been addressed in numerous places in the past year along with other Pros/Cons for both 23andME and FTDNA's FF.

Only other thing that I can say is that I haven't had a materially higher rate of identifying actual relationships for one versus the other, but have had a couple more closer matches pop up in 23andMe, which you would expect, having a higher liklihood of such with the larger database. Of course that also comes down to the random luck of recombination and who tests with which company and even more random luck of whether you can contact them or not. May also depend on an individuals circumstances with regard to which test would be better, so if they can do both, that would probably be a fairly consensus recomendation. If FTDNA eventually offers an import option for 23andMe data for FF (at a nominal fee of course), the best course may be to purchase test with 23andme and then do the data import. Of course that will also depend on the pricing and individual needs.

[mkdexter]

Thanks for the links and info Paul.

Yes FTDNA would be very wise to move forward on the RF - FF import.

On the Affy conversion here's another twist. On DNA-forums there are some saying they have not seen their FF results converted yet. Doug McDonald is one. He has an Affy kit and no Illumina replacement for it.


mcdonald, on 27 April 2011 - 10:30 AM, said:
really?

I turned in my request at the very first and still no results.
I did have to send in another scraping, but they reported my full
111 markers results promptly. Something funny is going on.

Doug McDonald


Are all Affy conversions really done? Very interesting.