Hello all. I found out that BC15_Control is not in clinical data but it is in all other data. . Should I ignore it and proceed with the remaining 614 samples? Thank you.
Created by Jenny Empawi jaempawi Hi Abby @abby.vanderlinden, Thank you for your quick response! The RUSH center told that @yiyima worked on the QC using 2 parameters. Hope she will be able to provide the data soon so I can complete the Validation project. Hi @Sithara85, we do not currently have the RIN values for the ROSMAP monocyte RNAseq data. It was uploaded several years ago and was not provided at that time.
@yiyima, do you know if RIN or other QC info is available for the monocyte RNAseq? If so, I can add it to the assay metadata file for this study so it is available to AD Portal users. Hello, I am analyzing the monocyte RNAseq data. To do the QC analysis I would like to use the RIN, sequence/plate info, etc for the sequencing experiments. Is it available anywhere in synapse? I found the metadata file syn21088596 but that has RIN values NA for the monocyte RNAseq samples. Hi @jaempawi , the data contributor confirmed that this is a technical control sample. It can be included in QC but should not be included in analysis. Thanks for your patience -- I will add a note to the methods section on the wiki page! Thank you for your reply. Looking forward to hearing from soon! Ok, I suspect that this is a control sample, since there is no individual metadata. I'll contact the original data uploader and verify, and if this is the case I'll make sure to add a note to the metadata files and the methods description. I suspect you are fine excluding this sample from your analyses. I'll let you know what I hear from the data contributor!
Abby Hi Abby, thanks for replying. BC15_Control is found in syn21323366 but not in syn3191087. Therefore, when I merged them, it is excluded from the merged metadata. It is one of the ROSMAP metadata files and has the RNAseq fastq file. Looking forward to your reply. Hi there, can you clarify where you found the identifier "BC15_Control"? Was it as a file annotation on one of the data files, or in one of the ROSMAP metadata files?