Hi all, I downloaded the RNAseq read count data for dataset syn5049298 and syn5049298 (MayoRNAseq_RNAseq_CBE_geneCounts.tsv and MayoRNAseq_RNAseq_TCX_geneCounts.tsv). Now I want to extract AD samples from the matrix. Could you please help on how I can get the ID of AD samples? My second question is that if I want to get gene expression fpkm value, should I start with normalized gene count or just the un-normalized one? I will use edgeR and the corresponding gene length to calculate rpkm value, please correct me if this is not proper. Thank you all in advance.

Created by hangch
Dear https://www.synapse.org/#!Profile:3347449 The information regarding which samples are AD can be found in the covariate files: CBE: https://www.synapse.org/#!Synapse:syn5223705 TCX: https://www.synapse.org/#!Synapse:syn3817650 You can also find information about which samples to exclude based on quality control, found here: CBE: https://www.synapse.org/#!Synapse:syn6126119 TCX: https://www.synapse.org/#!Synapse:syn6126114 I will let Cory answer your question regarding gene counts. Mariet
Dear @hangch, Thank you for the question. @mxa24 or @coryfunk, can you answer this question? Thanks, Ben

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