Aclust package: IlluminaHumanMethylation450kCHR37 not found
Entering edit mode
Last seen 4.5 years ago


I want to use A clustering to find DMRs, with Aclust package. My problem is that Aclust uses IlluminaHumanMethylation450k.db package, which is deprecated, therefore when I'm trying to use a command:

ordered =

I get following error (partially it's in Polish, but the most important part is visivle I believe):

Error in as.list(IlluminaHumanMethylation450kCHR37[probe.vec]) :
  błąd podczas obliczania argumentu 'x' przy wybieraniu metody dla funkcji 'as.list': Error: object 'IlluminaHumanMethylation450kCHR37' not found


Does anyone have some ideas, advices how to solve this problem? I am quite determined to use Aclust, I know there is also Python version, but I assume there may be similar problems.


Thanks in advance,


illuminahumanmethylation450k.db aclust methylation annotation illumina • 1.3k views
Entering edit mode
Last seen 6 hours ago
United States

This support site is for Bioconductor packages. The Aclust package seems to be sort of orphaned. I don't see that it even exists on Tamar Sofer's original website, and the only version around seems to be what Pete Hickey has in his GitHub repo. But since it isn't a Bioc package anyway, this is not the place to be asking for help.

You can

  1. Talk to Pete directly and see if he has some workaround that he is using.
  2. Talk to Tamar Sofer and ask him what's up.
  3. Clone Pete's GitHub repo and make it work using the FDb.InfiniumMethylation.hg19 package instead of the (deprecated and busted besides) IlluminaHumanMethylation450k.db package. That might be a fun project.
  4. Use a sufficiently old version of R/Bioconductor that will still install the IlluminaHumanMethylation450k.db package. That might be the easiest thing to do, but it's probably also the most boring as well.
Entering edit mode

Jim's covered your main options. Just adding that I haven't tried to use Aclust in quite some time and don't have a version with proper 450k annotation support nor do I plan to make one.

It sounds like you've come across this, but in case you haven't, Brent Pedersen re-implemented the Aclust algorithm in Python ( He also wrote the Python software, 'crystal', that integrates with his version of aclust for downstream associated testing of the clusters with phenotype ( Since these are written in Python, they obviously don't directly depend on the IlluminaHumanMethylation450k.db package. So you might also have 

5. Use aclust/crystal Python software to perform a similar analysis

This comes with the proviso that it looks like Brent is no longer actively developing aclust/crystal - but then it sounds like the original Aclust is somewhat abandoned and Brent is generally a very responsive and helpful developer.

Entering edit mode

Thank you very much! Answers from both of you were very useful - at leat I know what options do I have now. Thanks a lot once again!

Entering edit mode
Last seen 6.0 years ago


The online platform has become highly competitive for new businesses to establish their brand and visibility online to reach out the targeted customers to promote their products or services. Hence it has become mandatory to lookout for other online marketing techniques that increases traffic to your website to generate the business revenues. As online promotion through your website is not enough you can now check out with the buy ceo email lists that helps you to reach out various client base that you have not yet touched as part of your marketing strategies. Moreover, if you are having a global business you can easily have access across the globe through targeted email lists to promote your business on the international level.

You can buy targeted email list of worldwide, US email list, UK email list, Australia email list and so on depending on the audience that you would like to reach out for your business. There are many advantages with the buy email lists for marketing as they are quiet affordable compared to other marketing medium like newspapers, billboards, radio ads, print advertising etc which are very expensive but you cannot know the mileage actually generated by them. Here as you send the emails to the targeted audience you can be sure about 20 to 50% returns on your promotion investments and is also an easy way to reach out targeted audience. You can also in fact track the emails and also have a feedback from the customers by including a form and also check out for the visitors who have actually visited your site using the backup links on the emails.

However, to become successful with the email marketing strategy it is important that you find reliable company who offer genuine and regularly updated list of email addresses of people by filtering who are really interested in your business products or services. The companies offering to buy targeted email list services also take up the responsibility of actually forwarding your newsletters to the people and tracking the mileage generated by them leaving you to concentrate on other aspects of your business while they increase the traffic to your websites.

So based on the regions that you would like to promote your brand check out for the various email database packages offered in affordable prices to enjoy the leads generated through this bulk online email marketing techniques.






Login before adding your answer.

Traffic: 272 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6