Hi, In syn6090805, is Dx.Beta = the difference in mean expression between control and AD or the log fold difference between the conditions? Thanks!

Created by dmay
@mxa24 - can you please take a look at the question above. Thanks for your help!
Hi, Thank you for your quick reply. I hope you can help me with a few additional questions: 1) In the DifferentialExpression analyses syn7332090 and syn6090802 , it says ? Files and folders with the ?Additional_QC? flag reflect results following removal of both category ?A? and ?B? samples. Those without the flag reflect results following removal of category ?A? samples only.? Although it seems that samples failing both A and B QC stages were excluded from the TCX and CBE CQN files, these files are not tagged as having both A and B samples removed. I would just like to confirm - Were both A and B samples removed from the CQN files (syn15889850 and syn15833248) used for differential gene expression analyses? And were these the only samples that were removed? 2) Would you recommend removing both A and B samples (e.g. indicated in syn6126114) from the CPM data (e.g. syn5201007) before downstream analysis on these samples? 3) Regarding your first answer, I searched the cited literature and as I understand, CQN normalization returns normalized counts on the log2-scale, which means the Dx.Beta column reported is equivalent to log2-fold changes. Could you indicate whether I am correct in this understanding? Thank you in advance for your time.
See reference 3 and 4 here for more information about the differential expression methods: syn6090802

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