Error in mvregmed.grid(): invalid alpha estimates #1
Description
Hi,
I used regmed.grid to check whether the effect of an exposure (x1) over an outcome (y1) is mediated by multiple mediators (mediators).
fit.grid_single <- regmed.grid(x1, mediators, y1, lambda_grid, frac.lasso = 0.8)
> lambda_grid <- seq(from = 0.4, to = 0.01, by = -0.05)
> head(x1) #Sex dummy (0=male, 1=female)
[1] 0 0 1 1 1 1
> head(mediators) #CLR transformed cell type proportions (scaled/centered)
B_intermediate B_memory B_naive Plasmablast
[1,] -0.2230030 -0.71218298 -0.4023354 0.9098591
[2,] -0.2573671 0.09965716 1.8207424 -1.2761777
[3,] 0.0977724 -0.42916827 -0.5502540 0.6142060
[4,] 1.2688690 -0.43791283 0.7899916 -1.2816000
[5,] -0.5406937 0.24253059 0.5121418 -0.1433242
[6,] -0.7383424 0.32146709 -0.7942261 0.9634093
> head(y1) #gene expression of one gene (scaled/centered)
[,1]
[1,] -0.81420376
[2,] -0.87844074
[3,] 0.92019478
[4,] -0.05620736
[5,] 0.58616247
[6,] 0.29067235
> length(x1)
[1] 32
> dim(mediators)
[1] 32 4
> dim(y1)
[1] 32 1
I repeated the same per each of the outcomes in y, and for all of them alpha*beta!=0. However, when I use mvregmed.grid to consider the multiple outcomes at the same time (y) I get the following error:
fit.grid_mult <- mvregmed.grid(x, mediators, y, lambda_grid)
Error in mvregmed.grid(x, mediators, y, lambda_grid) :
invalid alpha estimates"
I don't get where the issue can come from, since in the test for each independent outcome using regmed.grid it can estimate the alpha in all cases.
Notice that all variables (x, mediators and y) are scaled and centered, as recommended in your vignette. Also, if I've tried mvregmed.grid with a continuous exposure (Age scaled/centered) and it is working...
> head(x) #Sex dummy (0=male, 1=female) --> in matrix format as `mvregmed.grid` requires it
Sex
[1,] 0
[2,] 0
[3,] 1
[4,] 1
[5,] 1
[6,] 1
> head(mediators) #CLR transformed cell type proportions (scaled/centered)
B_intermediate B_memory B_naive Plasmablast
[1,] -0.2230030 -0.71218298 -0.4023354 0.9098591
[2,] -0.2573671 0.09965716 1.8207424 -1.2761777
[3,] 0.0977724 -0.42916827 -0.5502540 0.6142060
[4,] 1.2688690 -0.43791283 0.7899916 -1.2816000
[5,] -0.5406937 0.24253059 0.5121418 -0.1433242
[6,] -0.7383424 0.32146709 -0.7942261 0.9634093
> head(y) #gene expression of different genes (scaled/centered)
XIST RPS4X EIF1AX EIF2S3 DDX3X MARCKS
[1,] -0.81420376 -0.3351344 -0.9793981 -0.384665761 -0.6400417 -0.7830787
[2,] -0.87844074 -1.0670184 -0.9249871 -0.858100544 -0.8360354 -1.2021912
[3,] 0.92019478 1.1646280 1.0066036 1.004076268 0.4869217 1.0036642
[4,] -0.05620736 -0.3691290 -0.3808771 -0.132167210 -0.2358048 0.2977905
[5,] 0.58616247 1.0666435 1.1154257 1.067200906 0.8911586 0.5404346
[6,] 0.29067235 0.2497729 0.1904385 -0.005917935 -0.3583009 0.1433806
STT3B SDF4 CD99 TMED10 NAP1L1 NDUFB7
[1,] -0.22999538 0.007225538 -0.3516680 0.51016032 -0.4241517 -0.3044673
[2,] -0.92331480 -0.609353688 -0.8187893 -0.94389986 -1.0429747 -0.9019126
[3,] 0.14333046 0.777949569 0.9222992 1.10500312 1.5698338 1.5338259
[4,] -0.65665349 -0.532281284 -0.4790647 -0.61343164 -0.2728838 -0.4882966
[5,] 0.08999819 0.161370344 0.7524369 -0.08468248 1.0885270 0.1091487
[6,] -0.06999860 0.161370344 0.5825746 -0.24991659 -0.1078643 -0.1665953
IFNGR2 AC016831.7 ATP2B1 CD37 SKIL OFD1
[1,] -0.85016389 0.365188047 -0.5656745 -0.42888983 -0.44038086 -0.5637288
[2,] -0.85016389 -1.118750684 -0.9519482 -0.94375265 -0.96291851 -1.0147119
[3,] 0.50633030 0.550680388 0.8861818 1.23531322 0.70267026 1.1399849
[4,] -0.09655601 -0.376781318 -0.2193602 -0.01803970 -0.42405155 -0.3131827
[5,] 1.18457739 0.179695706 0.8329027 1.43293733 0.84963398 1.2402034
[6,] 0.20488714 -0.005796636 0.2201927 -0.02324034 0.01683959 -0.1127458
> dim(x)
[1] 32 1
> dim(mediators)
[1] 32 4
> dim(y)
[1] 32 18
> str(x)
num [1:32, 1] 0 0 1 1 1 1 1 1 1 1 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr "Gender"
> str(mediators)
num [1:32, 1:4] -0.223 -0.2574 0.0978 1.2689 -0.5407 ...
- attr(*, "scaled:center")= Named num [1:4] -2.95e-17 -3.38e-17 -4.29e-17 2.78e-17
..- attr(*, "names")= chr [1:4] "B_intermediate" "B_memory" "B_naive" "Plasmablast"
- attr(*, "scaled:scale")= Named num [1:4] 1 1 1 1
..- attr(*, "names")= chr [1:4] "B_intermediate" "B_memory" "B_naive" "Plasmablast"
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:4] "B_intermediate" "B_memory" "B_naive" "Plasmablast"
> str(y)
num [1:32, 1:18] -0.8142 -0.8784 0.9202 -0.0562 0.5862 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:18] "XIST" "RPS4X" "EIF1AX" "EIF2S3" ...
- attr(*, "scaled:center")= Named num [1:18] 68.4 1324.2 49 40.2 83.2 ...
..- attr(*, "names")= chr [1:18] "XIST" "RPS4X" "EIF1AX" "EIF2S3" ...
- attr(*, "scaled:scale")= Named num [1:18] 77.8 1000.2 36.8 31.7 81.6 ...
..- attr(*, "names")= chr [1:18] "XIST" "RPS4X" "EIF1AX" "EIF2S3" ...
Thanks in advance!
Aida