Hi, I had downloaded differentialExpressionSummary.tsv from https://www.synapse.org/#!Synapse:syn14237651, and had following two questions: 1. Where can I find the description about the model such as "Diagnosis.Sex" and "Diagnosis.AOD"? 2. For each comparison, how could I find the sample size? For example, for this comparison "model: Diagnosis.Sex ; Tissue: CBE; Comparison: AD-CONTROL ; Sex: FEMALE", how can I find the sample size for AD and control individuals respectively? Thanks, Gangcai

Created by Gangcai Xie gangcai
Hello @th_vairam and @jgockley, how do I find information regarding the sample sizes for all 7 tissues? Which synapse files to look for and what conditions to filter? I understand from the above discussion that syn11024258 is for the ROSMAP DLPFC. Looking for the other 6 tissues (CBE, TCX, FP, IFG, STG, PHG) Thanks! Any lead is appreciated.
Hi, I am working on some QC analysis for blood monocyte based RNAseq data. Could you tell me where can I find the Qc parameters such as PCT_RIBOSOMAL_BASES, MEDIAN_3PRIME_BIAS, RIN etc? Thank you, Sithara
I'd like to cite the data used from All Differential Expression (Merged). Is there a publication or a pre-print for it? If not I'd simply put synapse id (Synapse:syn14237651)? Or, is there citation for ROS/MAP and Mayo clinic that were used in these data?
Hello @wangtaifr Sorry for the delayed response. The covariates file ```syn11024258``` for the ROSMAP DLPFC expression data lists case vs control by sex as: ``` AD.FEMALE = 109 CONTROL.FEMALE = 47 OTHER.FEMALE = 248 AD.MALE = 46 CONTROL.MALE = 39 OTHER.MALE = 143 ``` Everything lines up except your reported 37(F) controls! We defined cases and controls in the ROSMAP Cohort by the following criteria: ``` Cases: BRAAK Score > 3 CERAD < 3 **and** CogDX (cognitive diagnosis of probable AD with no other causes) = 4 Controls: BRAAK l < 4 CERAD > 2 **and** CogDX (cognitive diagnosis of ?no cognitive impairment?) = 1 ``` Individuals which did not fall into either classification are denoted as other.
Hello @th_vairam We are looking into the Differential Expression Table and are focusing on DLPFC dataset with Comparison = "AD-CONTROL" and ALL sex. Could you confirm if the number of individuals (AD vs Control) in our subset are what you provided in the table: ROSMAP DLPFC (AD=109(F)+46(M) versus 37(F)+39(M)? Many thanks
Hi @fanc232 , you can find the batch information here syn4300313. NCI/MCI/AD is the disease status and not technical batch.
Excuse me, @th_vairam , could you please tell me where can I find information of "experimental batch" of the ROSMAP bulkRNAseq data? I am new to gene analysis and to remove potential batch effect, I used ComBat in sva package with the parameter 'batch' set as NCI/MCI/AD, and the 'dat' set as syn8691134, however, using h_clust, I found no improvement. So I think set 'batch' as NCI/MCI/AD should be wrong. But I failed to find the experimental batch information.
Hi, I have a question about the 'Direction'. It's easy to understand UP or Down, but I saw some genes with a quite small P.value or adj.P.Val and 'Direction' labeled as "NONE"? Does "NONE" mean that gene is not identified as a differentially expressed gene? Thanks very much, Zhen
Thanks!
Yes, your interpretations are correct @rjim7242
Hi, I have a question related to what is described above in Thanneer's reply. For the Diagnosis.Sex term (described as a "colinear model of both Diagnosis and Sex"), I read on the data set's main page that this represents the formula "Gene expression = Diagnosis x Sex + covariates + (1/Donor)". Just to be sure, does this model described test for an interaction between diagnosis and sex (male or female)? I presume this is the case based on the results and description but want to ask to be sure I'm understanding and presenting the data correctly when sharing results with peers. Thanks very much, Jim
Hello @gangcai Thank you for your query. We are currently working to release all the relevant analysis that were performed to obtain this differential expression results. Meanwhile, here are the quick answers to your questions. 1. Model descriptions are as follows All our analysis were performed for each gene with a weighted linear model. i.e., Gx = Dx + other covariates + error. Where Dx could be one of the following * SourceDiagnosis: These are diagnosis definitions (like CDR, Cogdx, Braak Pathology, etc.) from our source studies ROSMAP, MSSM, and Mayo * Diagnosis: We harmonized the AD and control definitions by defining cognitive scores, Braak staging, and tau pathology * APOE4: Number of apoe4 alleles (0,1,2) * Diagnosis.Sex: a colinear model of both Diagnosis and Sex * Diagnosis.AOD: a colinear model of both Diagnosis and age at death 2. Sample sizes are as follows Study|No of individuals|Tissue|AD||Control||Total No. of Samples |||Female|Male|Female|Male| MAYO|179|CBE|47|32|35|37|151 ||TCX|49|31|35|36|151 MSSM|164|FP|63|27|23|22|135 ||IFG|55|24|17|20|116 ||PHG|47|18|18|20|103 ||STG|57|28|20|17|122 ROSMAP|241|DLPFC|109|46|47|39|241 Total|584||318|160|148|152|778

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