# Binned value of expression - difficulty replicating distribution **URL:** \ **Category:** Technical Support\ **Tags:** expression-atlas\ **Created:** [21 April 2025 09:03 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773 "2025-04-21T09:03:26Z")\ **Posts on this page:** 16\ **Page:** 1
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [21 April 2025 09:03 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/1 "2025-04-21T09:03:26Z")
If you download the binned gene expression data from open targets, values are distributed across the bins with the majority of values in bin 1-4 and then some in 5 and a small number in the higher bins. If I try and replicate this binning strategy with other data from Expression atlas I find nearly all the values are in bin 1. Reading the docs on Computational pipelines and datasets (RNA expression meta-analysis) I can see that the normalisation used might be different (I don’t think iRAP is using RUV) but I do not think that would be expected to change the distribution so dramatically? Particularly considering I’m comparing Expression Atlas TPMs to these TPMs. The only way I can make the distribution comparable is if I log transform (log2) the expression values. I can see no mention of such a transformation the docs - am I missing this somewhere? Do you log transform the expression data? Any input would be much appreciated & apologies if I have missed something in the documentation! ---
**Author:** ![Tobi\_Alegbe](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/tobi_alegbe/32/747_2.png) [@Tobi\_Alegbe](https://community.opentargets.org/u/Tobi_Alegbe)\ **Post date:** [24 April 2025 09:54 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/2 "2025-04-24T09:54:25Z")
Hi Grace, You’re correct in identifying that this process isn’t particularly clear. Our baseline expression pipeline has remained untouched in many ways for several years now and we are in the process of revamping it to update the data, code and documentation (amongst other things!) so that the replication process is clearer to follow. I would expect this to be live later this year but cannot offer any promises. Until that time we cannot offer further assistance here unfortunately - apologies. Kind regards, Tobi ---
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [24 April 2025 10:08 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/3 "2025-04-24T10:08:29Z")
Hi Tobi, Excited to see the updates later in the year 🙂 There is no way you can confirm or deny whether the expression data is logged at any stage in the current process? Many thanks, Grace ---
**Author:** ![Tobi\_Alegbe](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/tobi_alegbe/32/747_2.png) [@Tobi\_Alegbe](https://community.opentargets.org/u/Tobi_Alegbe)\ **Post date:** [24 April 2025 10:35 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/4 "2025-04-24T10:35:37Z")
Unfortunately not, I don’t have access to the code which generated the data. This is a large motivator for the refactoring. By the end of the year the whole process should be open source and clearly documented. Sorry that I cannot help further in this regard. Best, Tobi ---
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [24 April 2025 10:49 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/5 "2025-04-24T10:49:09Z")
Ok thanks Tobi, I appreciate the candor. Best of luck with the refactor! BW, Grace ---
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [22 July 2025 07:49 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/6 "2025-07-22T07:49:36Z")
Hi Tobi! Is there any update here? BW, Grace ---
**Author:** ![Tobi\_Alegbe](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/tobi_alegbe/32/747_2.png) [@Tobi\_Alegbe](https://community.opentargets.org/u/Tobi_Alegbe)\ **Post date:** [29 July 2025 21:38 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/7 "2025-07-29T21:38:00Z")
Hi Grace, Yes we are still aiming to have this ready by the end of the year. We are on track for inclusion in the September release but I cannot offer any guarantees that this will certainly be the case. I can however assure you that revamping this area is currently a top priority both for myself and for others in the Open Targets team. All the best, Tobi ---
**Author:** ![Tobi\_Alegbe](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/tobi_alegbe/32/747_2.png) [@Tobi\_Alegbe](https://community.opentargets.org/u/Tobi_Alegbe)\ **Post date:** [10 September 2025 15:26 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/8 "2025-09-10T15:26:48Z")
Just an update on this, whilst we were on track for a September release we’ve made the decision to delay this until the end of the year to iron out some kinks we weren’t completely satisfied with. I noticed your original post referenced the meta-analysis data specifically. Just so you’re aware the intent is not to include a true meta-analysis at this point, rather to focus on harmonising a select few representative public datasets across several modalities. Just so you don’t have the wrong impression in what to expect. ---
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [10 September 2025 15:44 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/9 "2025-09-10T15:44:33Z")
Hi Tobi, Thank you so much for keeping us posted, we appreciate it! ---
**Author:** ![Tobi\_Alegbe](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/tobi_alegbe/32/747_2.png) [@Tobi\_Alegbe](https://community.opentargets.org/u/Tobi_Alegbe)\ **Post date:** [6 January 2026 12:26 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/10 "2026-01-06T12:26:49Z")
For the end of year release mentioned above we made the decision to provide early access to the updated baseline expression data and new widget exclusively to our partners via our [https://partner-platform.opentargets.org/](https://partner-platform.opentargets.org/) which is available to our five pharmaceutical and two academic institute partners. The new widget and data will be made available to the public in our March release. Hope that’s helpful. Let me know if there are any further questions. Tobi ---
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [8 January 2026 09:56 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/11 "2026-01-08T09:56:33Z")
Thanks Tobi! I appreciate you taking the time to keep us posted ---
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [1 April 2026 06:12 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/12 "2026-04-01T06:12:32Z")
Hello Tobi! I hope you’re well. We couldn’t see the data in the March release? ---
**Author:** ![hcornu](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/hcornu/32/716_2.png) [@hcornu](https://community.opentargets.org/u/hcornu)\ **Post date:** [11 May 2026 09:24 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/13 "2026-05-11T09:24:49Z")
Hi @graceLBI! We’ve made the decision to push back the release of the baseline expression widget, likely to our June release. I’ll let you know when it’s out! ---
**Author:** ![graceLBI](https://avatars.discourse-cdn.com/v4/letter/g/ecd19e/32.png) [@graceLBI](https://community.opentargets.org/u/graceLBI)\ **Post date:** [11 May 2026 09:38 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/14 "2026-05-11T09:38:05Z")
Thank you very much Helena! ---
**Author:** ![Tobi\_Alegbe](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/tobi_alegbe/32/747_2.png) [@Tobi\_Alegbe](https://community.opentargets.org/u/Tobi_Alegbe)\ **Post date:** [25 June 2026 22:51 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/15 "2026-06-25T22:51:49Z")
Thanks Helena!. Sorry I missed that comment, Grace. You can find the data in our release as of today and if you have an issues with it feel free to let me know! The code to reproduce it from public sources is all available on our github too. ---
**Author:** ![Conflict\_Analysics](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/conflict_analysics/32/985_2.png) [@Conflict\_Analysics](https://community.opentargets.org/u/Conflict_Analysics)\ **Post date:** [3 August 2026 09:37 UTC](https://community.opentargets.org/t/binned-value-of-expression-difficulty-replicating-distribution/1773/16 "2026-08-03T09:37:26Z")
Hey, Open Targets’ binned expression values are usually based on a transformed scale (often log-based) after their meta-analysis pipeline, which is why most values sit in the lower bins. Raw or simply normalized TPMs from Expression Atlas will look very different and pile up in bin 1 unless you apply a similar transformation.