From b1db6d8f1b6050bc5358c34c1031c2c9276c8d70 Mon Sep 17 00:00:00 2001
From: yuhanH <yh1970@nyu.edu>
Date: Thu, 7 Oct 2021 11:43:09 -0400
Subject: [PATCH 1/3] not center query lsi embeddings

---
 R/integration.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/integration.R b/R/integration.R
index 81c34006b..62150ed1b 100644
--- a/R/integration.R
+++ b/R/integration.R
@@ -1041,7 +1041,7 @@ FindTransferAnchors <- function(
         reduction = query[[reference.reduction]],
         data = GetAssayData(object = reference, assay = reference.assay, slot = "data"),
         mode = "lsi",
-        do.center = TRUE,
+        do.center = FALSE,
         do.scale = FALSE,
         use.original.stats = FALSE,
         verbose = verbose
@@ -1053,7 +1053,7 @@ FindTransferAnchors <- function(
         reduction = reference[[reference.reduction]],
         data = GetAssayData(object = query, assay = query.assay, slot = "data"),
         mode = "lsi",
-        do.center = TRUE,
+        do.center = FALSE,
         do.scale = FALSE,
         use.original.stats = FALSE,
         verbose = verbose

From 07383a0ed9553b8bca544723b24ea354f62a80c1 Mon Sep 17 00:00:00 2001
From: yuhanH <yh1970@nyu.edu>
Date: Thu, 7 Oct 2021 11:51:55 -0400
Subject: [PATCH 2/3] add News

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 8fcea6c95..2d897c06b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -13,6 +13,7 @@
 - Add `ReadParsebio()` function to read output from Parse Biosciences
 - Add the `image.alpha` parameter to `SpatialDimPlot()` and `SpatialFeaturePlot()`
 - Add support for the correlation metric in `RunUMAP` ([#4972](https://github.com/satijalab/seurat/issues/4972))
+- Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` 
 
 ## Changes
 - Warn and continue rather than erroring if not all features are available in `FindSpatiallyVariableFeatures()` ([#4611](https://github.com/satijalab/seurat/issues/4611))

From 297764caa21957255631a157049c88e1167a2e01 Mon Sep 17 00:00:00 2001
From: timoast <4591688+timoast@users.noreply.github.com>
Date: Thu, 7 Oct 2021 14:14:14 -0400
Subject: [PATCH 3/3] Update dev version

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ff8a7108f..1d948cb18 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.4.9002
-Date: 2021-09-10 
+Version: 4.0.4.9003
+Date: 2021-10-07
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(