Hello,
Could you please provide some more details on whether and/or how normalization was performed for these lipidomics data? It's unclear to me whether normalization with the deuterium standards has already been performed and values can be compared between biological specimens or whether that normalization is still outstanding.
Thanks for your help!
Created by dmay Thank you very much @emory-cyc ! Dear @djuna Sorry that it takes longer than I expected, but I am working on it. Will let you know soon this week. Dear @emory-cyc and @abby.vanderlinden, I just wanted to check in and ask whether you were able to upload the data - If so, where could I access it? Many thanks in advance! Thank you so much @emory-cyc for your time with this!
Hi @djuna ! Sorry for being slow due to my busy schedule. I will try to upload lipid search raw data this week and leave the message here. Hi @emory-cyc ! I just wanted to ask when you think you might be able to upload the data, so I can plan my analysis. Thank you very much! @abby.vanderlinden @emory-cyc Thank you very much! @emory-cyc It would be great to have the raw data!
I have given you upload permission to the Staging folder for this study -- you can upload any additional files to syn29574358. Please contact me either in this thread or via email at abby.vanderlinden@sagebase.org when you have uploaded the files, and I will verify that we have appropriate metadata for them before releasing them.
@djuna @lilunho I will make sure to update you here when the raw data is available in the AD Knowledge Portal! Thank you. Hi!
I can provide the raw data directly exported from LS.
@abby.vanderlinden
If I would like to post the raw data to Synapse, is there any instruction I need to follow?
Thank you. Hi @abby.vanderlinden , I just wanted to follow-up on this thread. Would it be possible to have access to the raw data and/or the lipidsearch-processed data prior to batch correction? Thank you for your help in advance. Hi @emory-cyc! Sorry to bother you again. Would it be possible to have access to the raw data and/or the lipidsearch-processed data prior to batch correction? Many thanks.
Hi @djuna, it is good to have internal to do further normalization; however, in our case, we did not detect all the internals in different lipid class as well as all the samples and hence, I couldn't normalize further. Instead, I did the batch correction based on the overall signal and QC. Thank you! Hi @emory-cyc Thank you so much for the reply. Just to add a clarification question - Are you saying that it's appropriate to compare the relative values in this data (ROSMAP_Brain_Lipidomic data_batch correction_combined Pos and Neg.csv) between samples without using the internal standards for further normalization or would you recommend conducting further normalization with the internal standards? Thank you very much for your time. Hi!
Sorry for the late response.
The normalization was not normalized by internal standards. The results were done with log 2 transformation and batch correction (dbnorm R package) for all the samples. The missing values were estimated for each feature by the lowest value detected for the corresponding feature. The data is not absolute concentration but these relative values can be used for further statistical analysis.
Hope this answered your question. Hi @djuna, I sent Chih-Yu an email as well -- I'll let you know as soon as I hear back. Thanks for your patience. Hi Abby,
Thanks for your quick reply. Is Emory-cyc an active user? Can I expect a response soon or is there someone else who might be able to help me?
Many thanks! @emory-cyc, do you have more information you can provide on the normalization for the [ROSMAP lipidomics data](https://www.synapse.org/#!Synapse:syn26475183), especially deuterium normalization?
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