@@ -269,25 +269,25 @@ score_matrix <- function(expr,

       # Max cor with quality factors.

       if (!is.null(qc_factors)) {

         EXP_QC_COR <-

-          EXP_QC_COR + cond_w * (1 - sum(unlist(apply(proj, 2, function(y) {

-            lm(y ~ qc_factors)$residual

-          })) ^ 2) / sum(scale(proj, scale = FALSE) ^ 2))

+          EXP_QC_COR + cond_w * (1 - sum(unlist(apply(proj[is_cond,], 2, function(y) {

+            lm(y ~ qc_factors[is_cond,])$residual

+          })) ^ 2) / sum(scale(proj[is_cond,], scale = FALSE) ^ 2))

       }

       # Max cor with UV factors.

       if (!is.null(uv_factors)) {

         EXP_UV_COR  <-

-          EXP_UV_COR + cond_w * (1 - sum(unlist(apply(proj, 2, function(y) {

-            lm(y ~ uv_factors)$residual

-          })) ^ 2) / sum(scale(proj, scale = FALSE) ^ 2))

+          EXP_UV_COR + cond_w * (1 - sum(unlist(apply(proj[is_cond,], 2, function(y) {

+            lm(y ~ uv_factors[is_cond,])$residual

+          })) ^ 2) / sum(scale(proj[is_cond,], scale = FALSE) ^ 2))

       }

       # Max cor with WV factors.

       if (!is.null(wv_factors)) {

         EXP_WV_COR <-

-          EXP_WV_COR + cond_w * (1 - sum(unlist(apply(proj, 2, function(y) {

-            lm(y ~ wv_factors)$residual

-          })) ^ 2) / sum(scale(proj, scale = FALSE) ^ 2))

+          EXP_WV_COR + cond_w * (1 - sum(unlist(apply(proj[is_cond,], 2, function(y) {

+            lm(y ~ wv_factors[is_cond,])$residual

+          })) ^ 2) / sum(scale(proj[is_cond,], scale = FALSE) ^ 2))

       }

     }