<—

cd /hpc/users/hoffmg01/www/dreamlet_analysis/PsychAD_r0

export OPENBLAS_NUM_THREADS=1

/sc/arion/projects/CommonMind/leed62/conda/envs/dreamlet430/bin/R –vanilla .libPaths(“/sc/arion/projects/CommonMind/leed62/conda/envs/dreamlet430/lib/R/library”)

system(“git pull”); rmarkdown::render(“PsychAD_r0_compare_methods.Rmd”)

—>

Load libraries

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## Loading required package: HDF5Array
## Loading required package: rhdf5
## 
## Attaching package: 'HDF5Array'
## The following object is masked from 'package:rhdf5':
## 
##     h5ls
## 
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Processing block [[1/1, 90/393]] ...
## OK
Processing block [[1/1, 91/393]] ... OK
Processing block [[1/1, 92/393]] ...
## OK
Processing block [[1/1, 93/393]] ... OK
Processing block [[1/1, 94/393]] ...
## OK
Processing block [[1/1, 95/393]] ... OK
Processing block [[1/1, 96/393]] ...
## OK
Processing block [[1/1, 97/393]] ... OK
Processing block [[1/1, 98/393]] ...
## OK
Processing block [[1/1, 99/393]] ... OK
Processing block [[1/1, 100/393]] ...
## OK
Processing block [[1/1, 101/393]] ... OK
Processing block [[1/1, 102/393]] ...
## OK
Processing block [[1/1, 103/393]] ... OK
Processing block [[1/1, 104/393]] ...
## OK
Processing block [[1/1, 105/393]] ... OK
Processing block [[1/1, 106/393]] ...
## OK
Processing block [[1/1, 107/393]] ... OK
Processing block [[1/1, 108/393]] ...
## OK
Processing block [[1/1, 109/393]] ... OK
Processing block [[1/1, 110/393]] ...
## OK
Processing block [[1/1, 111/393]] ... OK
Processing block [[1/1, 112/393]] ...
## OK
Processing block [[1/1, 113/393]] ... OK
Processing block [[1/1, 114/393]] ...
## OK
Processing block [[1/1, 115/393]] ... OK
Processing block [[1/1, 116/393]] ...
## OK
Processing block [[1/1, 117/393]] ... OK
Processing block [[1/1, 118/393]] ...
## OK
Processing block [[1/1, 119/393]] ... OK
Processing block [[1/1, 120/393]] ...
## OK
Processing block [[1/1, 121/393]] ... OK
Processing block [[1/1, 122/393]] ...
## OK
Processing block [[1/1, 123/393]] ... OK
Processing block [[1/1, 124/393]] ...
## OK
Processing block [[1/1, 125/393]] ... OK
Processing block [[1/1, 126/393]] ...
## OK
Processing block [[1/1, 127/393]] ... OK
Processing block [[1/1, 128/393]] ...
## OK
Processing block [[1/1, 129/393]] ... OK
Processing block [[1/1, 130/393]] ...
## OK
Processing block [[1/1, 131/393]] ... OK
Processing block [[1/1, 132/393]] ...
## OK
Processing block [[1/1, 133/393]] ... OK
Processing block [[1/1, 134/393]] ...
## OK
Processing block [[1/1, 135/393]] ... OK
Processing block [[1/1, 136/393]] ...
## OK
Processing block [[1/1, 137/393]] ... OK
Processing block [[1/1, 138/393]] ...
## OK
Processing block [[1/1, 139/393]] ... OK
Processing block [[1/1, 140/393]] ...
## OK
Processing block [[1/1, 141/393]] ... OK
Processing block [[1/1, 142/393]] ...
## OK
Processing block [[1/1, 143/393]] ... OK
Processing block [[1/1, 144/393]] ...
## OK
Processing block [[1/1, 145/393]] ... OK
Processing block [[1/1, 146/393]] ...
## OK
Processing block [[1/1, 147/393]] ... OK
Processing block [[1/1, 148/393]] ...
## OK
Processing block [[1/1, 149/393]] ... OK
Processing block [[1/1, 150/393]] ...
## OK
Processing block [[1/1, 151/393]] ... OK
Processing block [[1/1, 152/393]] ...
## OK
Processing block [[1/1, 153/393]] ... OK
Processing block [[1/1, 154/393]] ...
## OK
Processing block [[1/1, 155/393]] ... OK
Processing block [[1/1, 156/393]] ...
## OK
Processing block [[1/1, 157/393]] ... OK
Processing block [[1/1, 158/393]] ...
## OK
Processing block [[1/1, 159/393]] ... OK
Processing block [[1/1, 160/393]] ...
## OK
Processing block [[1/1, 161/393]] ... OK
Processing block [[1/1, 162/393]] ...
## OK
Processing block [[1/1, 163/393]] ... OK
Processing block [[1/1, 164/393]] ...
## OK
Processing block [[1/1, 165/393]] ... OK
Processing block [[1/1, 166/393]] ...
## OK
Processing block [[1/1, 167/393]] ... OK
Processing block [[1/1, 168/393]] ...
## OK
Processing block [[1/1, 169/393]] ... OK
Processing block [[1/1, 170/393]] ...
## OK
Processing block [[1/1, 171/393]] ... OK
Processing block [[1/1, 172/393]] ...
## OK
Processing block [[1/1, 173/393]] ... OK
Processing block [[1/1, 174/393]] ...
## OK
Processing block [[1/1, 175/393]] ... OK
Processing block [[1/1, 176/393]] ...
## OK
Processing block [[1/1, 177/393]] ... OK
Processing block [[1/1, 178/393]] ...
## OK
Processing block [[1/1, 179/393]] ... OK
Processing block [[1/1, 180/393]] ...
## OK
Processing block [[1/1, 181/393]] ... OK
Processing block [[1/1, 182/393]] ...
## OK
Processing block [[1/1, 183/393]] ... OK
Processing block [[1/1, 184/393]] ...
## OK
Processing block [[1/1, 185/393]] ... OK
Processing block [[1/1, 186/393]] ...
## OK
Processing block [[1/1, 187/393]] ... OK
Processing block [[1/1, 188/393]] ...
## OK
Processing block [[1/1, 189/393]] ... OK
Processing block [[1/1, 190/393]] ...
## OK
Processing block [[1/1, 191/393]] ... OK
Processing block [[1/1, 192/393]] ...
## OK
Processing block [[1/1, 193/393]] ... OK
Processing block [[1/1, 194/393]] ...
## OK
Processing block [[1/1, 195/393]] ... OK
Processing block [[1/1, 196/393]] ...
## OK
Processing block [[1/1, 197/393]] ... OK
Processing block [[1/1, 198/393]] ...
## OK
Processing block [[1/1, 199/393]] ... OK
Processing block [[1/1, 200/393]] ...
## OK
Processing block [[1/1, 201/393]] ... OK
Processing block [[1/1, 202/393]] ...
## OK
Processing block [[1/1, 203/393]] ... OK
Processing block [[1/1, 204/393]] ...
## OK
Processing block [[1/1, 205/393]] ... OK
Processing block [[1/1, 206/393]] ...
## OK
Processing block [[1/1, 207/393]] ... OK
Processing block [[1/1, 208/393]] ...
## OK
Processing block [[1/1, 209/393]] ... OK
Processing block [[1/1, 210/393]] ...
## OK
Processing block [[1/1, 211/393]] ... OK
Processing block [[1/1, 212/393]] ...
## OK
Processing block [[1/1, 213/393]] ... OK
Processing block [[1/1, 214/393]] ...
## OK
Processing block [[1/1, 215/393]] ... OK
Processing block [[1/1, 216/393]] ...
## OK
Processing block [[1/1, 217/393]] ... OK
Processing block [[1/1, 218/393]] ...
## OK
Processing block [[1/1, 219/393]] ... OK
Processing block [[1/1, 220/393]] ...
## OK
Processing block [[1/1, 221/393]] ... OK
Processing block [[1/1, 222/393]] ...
## OK
Processing block [[1/1, 223/393]] ... OK
Processing block [[1/1, 224/393]] ...
## OK
Processing block [[1/1, 225/393]] ... OK
Processing block [[1/1, 226/393]] ...
## OK
Processing block [[1/1, 227/393]] ... OK
Processing block [[1/1, 228/393]] ...
## OK
Processing block [[1/1, 229/393]] ... OK
Processing block [[1/1, 230/393]] ...
## OK
Processing block [[1/1, 231/393]] ... OK
Processing block [[1/1, 232/393]] ...
## OK
Processing block [[1/1, 233/393]] ... OK
Processing block [[1/1, 234/393]] ...
## OK
Processing block [[1/1, 235/393]] ... OK
Processing block [[1/1, 236/393]] ...
## OK
Processing block [[1/1, 237/393]] ... OK
Processing block [[1/1, 238/393]] ...
## OK
Processing block [[1/1, 239/393]] ... OK
Processing block [[1/1, 240/393]] ...
## OK
Processing block [[1/1, 241/393]] ... OK
Processing block [[1/1, 242/393]] ...
## OK
Processing block [[1/1, 243/393]] ... OK
Processing block [[1/1, 244/393]] ...
## OK
Processing block [[1/1, 245/393]] ... OK
Processing block [[1/1, 246/393]] ...
## OK
Processing block [[1/1, 247/393]] ... OK
Processing block [[1/1, 248/393]] ...
## OK
Processing block [[1/1, 249/393]] ... OK
Processing block [[1/1, 250/393]] ...
## OK
Processing block [[1/1, 251/393]] ... OK
Processing block [[1/1, 252/393]] ...
## OK
Processing block [[1/1, 253/393]] ... OK
Processing block [[1/1, 254/393]] ...
## OK
Processing block [[1/1, 255/393]] ... OK
Processing block [[1/1, 256/393]] ...
## OK
Processing block [[1/1, 257/393]] ... OK
Processing block [[1/1, 258/393]] ...
## OK
Processing block [[1/1, 259/393]] ... OK
Processing block [[1/1, 260/393]] ...
## OK
Processing block [[1/1, 261/393]] ... OK
Processing block [[1/1, 262/393]] ...
## OK
Processing block [[1/1, 263/393]] ... OK
Processing block [[1/1, 264/393]] ...
## OK
Processing block [[1/1, 265/393]] ... OK
Processing block [[1/1, 266/393]] ...
## OK
Processing block [[1/1, 267/393]] ... OK
Processing block [[1/1, 268/393]] ...
## OK
Processing block [[1/1, 269/393]] ... OK
Processing block [[1/1, 270/393]] ...
## OK
Processing block [[1/1, 271/393]] ... OK
Processing block [[1/1, 272/393]] ...
## OK
Processing block [[1/1, 273/393]] ... OK
Processing block [[1/1, 274/393]] ...
## OK
Processing block [[1/1, 275/393]] ... OK
Processing block [[1/1, 276/393]] ...
## OK
Processing block [[1/1, 277/393]] ... OK
Processing block [[1/1, 278/393]] ...
## OK
Processing block [[1/1, 279/393]] ... OK
Processing block [[1/1, 280/393]] ...
## OK
Processing block [[1/1, 281/393]] ... OK
Processing block [[1/1, 282/393]] ...
## OK
Processing block [[1/1, 283/393]] ... OK
Processing block [[1/1, 284/393]] ...
## OK
Processing block [[1/1, 285/393]] ... OK
Processing block [[1/1, 286/393]] ...
## OK
Processing block [[1/1, 287/393]] ... OK
Processing block [[1/1, 288/393]] ...
## OK
Processing block [[1/1, 289/393]] ... OK
Processing block [[1/1, 290/393]] ...
## OK
Processing block [[1/1, 291/393]] ... OK
Processing block [[1/1, 292/393]] ...
## OK
Processing block [[1/1, 293/393]] ... OK
Processing block [[1/1, 294/393]] ...
## OK
Processing block [[1/1, 295/393]] ... OK
Processing block [[1/1, 296/393]] ...
## OK
Processing block [[1/1, 297/393]] ... OK
Processing block [[1/1, 298/393]] ...
## OK
Processing block [[1/1, 299/393]] ... OK
Processing block [[1/1, 300/393]] ...
## OK
Processing block [[1/1, 301/393]] ... OK
Processing block [[1/1, 302/393]] ...
## OK
Processing block [[1/1, 303/393]] ... OK
Processing block [[1/1, 304/393]] ...
## OK
Processing block [[1/1, 305/393]] ... OK
Processing block [[1/1, 306/393]] ...
## OK
Processing block [[1/1, 307/393]] ... OK
Processing block [[1/1, 308/393]] ...
## OK
Processing block [[1/1, 309/393]] ... OK
Processing block [[1/1, 310/393]] ...
## OK
Processing block [[1/1, 311/393]] ... OK
Processing block [[1/1, 312/393]] ...
## OK
Processing block [[1/1, 313/393]] ... OK
Processing block [[1/1, 314/393]] ...
## OK
Processing block [[1/1, 315/393]] ... OK
Processing block [[1/1, 316/393]] ...
## OK
Processing block [[1/1, 317/393]] ... OK
Processing block [[1/1, 318/393]] ...
## OK
Processing block [[1/1, 319/393]] ... OK
Processing block [[1/1, 320/393]] ...
## OK
Processing block [[1/1, 321/393]] ... OK
Processing block [[1/1, 322/393]] ...
## OK
Processing block [[1/1, 323/393]] ... OK
Processing block [[1/1, 324/393]] ...
## OK
Processing block [[1/1, 325/393]] ... OK
Processing block [[1/1, 326/393]] ...
## OK
Processing block [[1/1, 327/393]] ... OK
Processing block [[1/1, 328/393]] ...
## OK
Processing block [[1/1, 329/393]] ... OK
Processing block [[1/1, 330/393]] ...
## OK
Processing block [[1/1, 331/393]] ... OK
Processing block [[1/1, 332/393]] ...
## OK
Processing block [[1/1, 333/393]] ... OK
Processing block [[1/1, 334/393]] ...
## OK
Processing block [[1/1, 335/393]] ... OK
Processing block [[1/1, 336/393]] ...
## OK
Processing block [[1/1, 337/393]] ... OK
Processing block [[1/1, 338/393]] ...
## OK
Processing block [[1/1, 339/393]] ... OK
Processing block [[1/1, 340/393]] ...
## OK
Processing block [[1/1, 341/393]] ... OK
Processing block [[1/1, 342/393]] ...
## OK
Processing block [[1/1, 343/393]] ... OK
Processing block [[1/1, 344/393]] ...
## OK
Processing block [[1/1, 345/393]] ... OK
Processing block [[1/1, 346/393]] ...
## OK
Processing block [[1/1, 347/393]] ... OK
Processing block [[1/1, 348/393]] ...
## OK
Processing block [[1/1, 349/393]] ... OK
Processing block [[1/1, 350/393]] ...
## OK
Processing block [[1/1, 351/393]] ... OK
Processing block [[1/1, 352/393]] ...
## OK
Processing block [[1/1, 353/393]] ... OK
Processing block [[1/1, 354/393]] ...
## OK
Processing block [[1/1, 355/393]] ... OK
Processing block [[1/1, 356/393]] ...
## OK
Processing block [[1/1, 357/393]] ... OK
Processing block [[1/1, 358/393]] ...
## OK
Processing block [[1/1, 359/393]] ... OK
Processing block [[1/1, 360/393]] ...
## OK
Processing block [[1/1, 361/393]] ... OK
Processing block [[1/1, 362/393]] ...
## OK
Processing block [[1/1, 363/393]] ... OK
Processing block [[1/1, 364/393]] ...
## OK
Processing block [[1/1, 365/393]] ... OK
Processing block [[1/1, 366/393]] ...
## OK
Processing block [[1/1, 367/393]] ... OK
Processing block [[1/1, 368/393]] ...
## OK
Processing block [[1/1, 369/393]] ... OK
Processing block [[1/1, 370/393]] ...
## OK
Processing block [[1/1, 371/393]] ... OK
Processing block [[1/1, 372/393]] ...
## OK
Processing block [[1/1, 373/393]] ... OK
Processing block [[1/1, 374/393]] ...
## OK
Processing block [[1/1, 375/393]] ... OK
Processing block [[1/1, 376/393]] ...
## OK
Processing block [[1/1, 377/393]] ... OK
Processing block [[1/1, 378/393]] ...
## OK
Processing block [[1/1, 379/393]] ... OK
Processing block [[1/1, 380/393]] ...
## OK
Processing block [[1/1, 381/393]] ... OK
Processing block [[1/1, 382/393]] ...
## OK
Processing block [[1/1, 383/393]] ... OK
Processing block [[1/1, 384/393]] ...
## OK
Processing block [[1/1, 385/393]] ... OK
Processing block [[1/1, 386/393]] ...
## OK
Processing block [[1/1, 387/393]] ... OK
Processing block [[1/1, 388/393]] ...
## OK
Processing block [[1/1, 389/393]] ... OK
Processing block [[1/1, 390/393]] ...
## OK
Processing block [[1/1, 391/393]] ... OK
Processing block [[1/1, 392/393]] ...
## OK
Processing block [[1/1, 393/393]] ... OK

Batch correction with Harmony

Process data: log2 CPM + voom precision weights

Variance Partitioning Analysis

How well does Harmony capture Pool effect?

Differential expression: dreamlet analysis

Limma

Volcano

##           assay           rho
## 1         Astro -0.1106018086
## 2         CD8_T -0.0597618058
## 3    EN_L2_3_IT  0.0001011405
## 4  EN_L3_5_IT_1  0.0266529018
## 5  EN_L3_5_IT_2  0.0088506676
## 6  EN_L3_5_IT_3 -0.0213755896
## 7    EN_L5_6_NP -0.0267136885
## 8      EN_L6_CT  0.0399349322
## 9      EN_L6_IT  0.0124880619
## 10        EN_NF -0.0923194723
## 11         Endo -0.0073923202
## 12    IN_ADARB2 -0.0020169418
## 13     IN_LAMP5  0.0271448360
## 14     IN_PVALB -0.0220996446
## 15 IN_PVALB_CHC  0.0238434492
## 16       IN_SST  0.0218882604
## 17       IN_VIP  0.0346761023
## 18    Micro_PVM -0.0233628832
## 19          OPC -0.0104063513
## 20        Oligo  0.0482571415
## 21           PC -0.0132100690
## 22         VLMC -0.0634520491

DESeq2

Volcano

##           assay          rho
## 1         Astro  0.027130981
## 2         CD8_T  0.092237681
## 3    EN_L2_3_IT -0.043548705
## 4  EN_L3_5_IT_1  0.037816120
## 5  EN_L3_5_IT_2 -0.019032427
## 6  EN_L3_5_IT_3 -0.047236169
## 7    EN_L5_6_NP -0.026682672
## 8      EN_L6_CT -0.007159323
## 9      EN_L6_IT -0.026607405
## 10        EN_NF -0.069674511
## 11         Endo  0.065385840
## 12    IN_ADARB2 -0.046244185
## 13     IN_LAMP5 -0.095349736
## 14     IN_PVALB -0.035879503
## 15 IN_PVALB_CHC  0.026575374
## 16       IN_SST -0.078426056
## 17       IN_VIP -0.076689282
## 18    Micro_PVM -0.044201013
## 19          OPC  0.012179463
## 20        Oligo -0.030741024
## 21           PC  0.030861776
## 22         VLMC -0.001773601