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Multiple testing correction #6

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nfancy opened this issue Feb 23, 2022 · 0 comments
Open

Multiple testing correction #6

nfancy opened this issue Feb 23, 2022 · 0 comments

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@nfancy
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nfancy commented Feb 23, 2022

Hi,

Thank you very much for this very useful package. We are using this for comparing the differential cell type proportion in single nuclei RNA sequencing data. A common example can be found here here. I was wondering do we need multiple testing correction for the p-values obtained from each of the cell types? For example see the summary below:

> summary(dirichlet_res)

Call:
DirichletReg::DirichReg(formula = dirichlet_dt ~ diagnosis + brain_region + sex + age + PMI + RIN,
data = sn_ct_prop)

Standardized Residuals:
              Min       1Q   Median       3Q     Max
Astro     -1.8915  -0.5861  -0.0432   0.4115  2.9265
Micro     -1.9210  -0.6087  -0.1745   0.4216  2.1042
Oligo     -3.8777  -1.2850  -0.0789   1.8296  5.8966
OPC       -1.3329  -0.6777  -0.2168   0.1330  4.8122
Vasc      -1.6562  -0.6634  -0.3561   0.2591  2.9518

------------------------------------------------------------------
Beta-Coefficients for variable no. 1: Astro
                  Estimate Std. Error z value Pr(>|z|)    
(Intercept)        1.37217    0.30822   4.452 8.51e-06 ***
diagnosisAD       -0.46457    0.18704  -2.484 0.013000 *  
brain_regionmTemp  0.16425    0.18080   0.908 0.363626    
brain_regionSSC    0.49240    0.17622   2.794 0.005202 ** 
sexM               0.81271    0.19663   4.133 3.58e-05 ***
age                0.45041    0.11205   4.020 5.83e-05 ***
PMI                0.04278    0.01148   3.727 0.000194 ***
RIN                0.29228    0.08503   3.437 0.000587 ***
------------------------------------------------------------------
Beta-Coefficients for variable no. 2: Micro
                  Estimate Std. Error z value Pr(>|z|)    
(Intercept)        0.40135    0.37210   1.079 0.280766    
diagnosisAD       -0.37726    0.20383  -1.851 0.064187 .  
brain_regionmTemp  0.06662    0.19641   0.339 0.734464    
brain_regionSSC    0.00659    0.19295   0.034 0.972755    
sexM               1.08002    0.23322   4.631 3.64e-06 ***
age                0.58778    0.12377   4.749 2.05e-06 ***
PMI                0.04783    0.01384   3.457 0.000547 ***
RIN                0.49261    0.09790   5.032 4.86e-07 ***
------------------------------------------------------------------
Beta-Coefficients for variable no. 3: Oligo
                  Estimate Std. Error z value Pr(>|z|)    
(Intercept)        2.00718    0.33585   5.976 2.28e-09 ***
diagnosisAD       -0.41222    0.19433  -2.121 0.033898 *  
brain_regionmTemp  0.05895    0.17865   0.330 0.741409    
brain_regionSSC    0.30981    0.17623   1.758 0.078757 .  
sexM               0.94630    0.21737   4.353 1.34e-05 ***
age                0.42127    0.11598   3.632 0.000281 ***
PMI                0.02792    0.01170   2.387 0.017000 *  
RIN                0.44467    0.07923   5.613 1.99e-08 ***
------------------------------------------------------------------
Beta-Coefficients for variable no. 4: OPC
                  Estimate Std. Error z value Pr(>|z|)    
(Intercept)        0.93467    0.34043   2.746 0.006041 ** 
diagnosisAD       -0.50381    0.19249  -2.617 0.008862 ** 
brain_regionmTemp  0.01828    0.19774   0.092 0.926360    
brain_regionSSC    0.23676    0.19280   1.228 0.219448    
sexM               0.77014    0.21564   3.571 0.000355 ***
age                0.33099    0.12007   2.757 0.005839 ** 
PMI                0.03451    0.01262   2.735 0.006246 ** 
RIN                0.12266    0.09404   1.304 0.192130    
------------------------------------------------------------------
Beta-Coefficients for variable no. 5: Vasc
                  Estimate Std. Error z value Pr(>|z|)   
(Intercept)       -0.08012    0.41009  -0.195  0.84510   
diagnosisAD       -0.31873    0.22023  -1.447  0.14783   
brain_regionmTemp -0.07216    0.24141  -0.299  0.76502   
brain_regionSSC    0.38433    0.23053   1.667  0.09548 . 
sexM               0.75324    0.24958   3.018  0.00254 **
age                0.38217    0.14067   2.717  0.00659 **
PMI                0.03057    0.01519   2.013  0.04412 * 
RIN                0.27600    0.12116   2.278  0.02273 * 
------------------------------------------------------------------
Significance codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Log-likelihood: 1564 on 104 df (462 BFGS + 2 NR Iterations)
AIC: -2921, BIC: -2718
Number of Observations: 52
Link: Log
Parametrization: common

So, if I extract the p-values for diagnosisAD for each cell type, do we need to do a multiple-testing correction. Thanks in advance.

Nurun

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