Dear AMP-AD maintainers, Am I correct to understand that MSBB_RNAseq_covariates.csv (syn6100548) contains the mapping of sample IDs (`barcode` column) to individual IDs (`individualIdentifier` column)? If so, why is there a discrepancy between this file and the RNAseq counts table? For example, there's a sample labeled `8615` in AMP-AD_MSBB_MSSM_IlluminaHiSeq2500_normalized_counts_September_2016.txt (syn7809023) that is not present in the `barcode` column of syn6100548. A related question: is there a table mapping BrainBank IDs used by the microarray files (syn3157699) to individual IDs used by the clinical covariates file (syn3205399)? I think the latter used to contain BrainBank IDs in the first column, but it was recently changed to be `individualIdentifier` creating a disconnect with the associated microarray data. Thank you, -Artem

Created by Artem Sokolov ArtemSokolov
Got it. Thank you so much. -Artem
Hi Artem, MSSM will update these as part of a larger QC of their data. We will update the community once that has been done through this discussion thread: https://www.synapse.org/#!Synapse:syn2580853/discussion/threadId=3000. Follow it and you will get a notice. Best, Mette
Hi Mette, Happy New Year! I notice that the MSBB Microarray data is still not available. Are there any updates? Thanks, -Artem
Thanks Artem, I now see the issue. That looks like the brain bank ids that need to be replaced. We will need to remove public access from those files until files with new identifiers have been uploaded. Appreciated that you noticed Best, Mette
Thank you for the clarification, Mette. Unfortunately, the sample key (syn4552846) doesn't quite capture the mapping I need. Take a look at syn3191107. Individual columns are annotated with integer keys (Brain Bank IDs?), and there is no mapping of these integers to individual IDs nor the original .cel filenames (which could then be mapped to individual IDs through the key you mentioned). -Artem
Hi Artem, The RNAseq covariate file should correspond to the bam files that have passed qc. We will look into the issue with the extra samples in the normalized counts file. Thanks for the heads up Regarding the MSBB_ArrayTissuePanel study. Please see the December notice under [data release updates](https://www.synapse.org/#!Synapse:syn2580853/wiki/409847) (you should have received an email regarding this if you have downloaded these files previously). The sample key (syn4552846) matches the new individual identifier to the filenames Let me know if that answers your questions Best, Mette

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