DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
0
0
Entering edit mode
Emily • 0
@d16c34b6
Last seen 16 months ago
United States

I have performed deconvolution of GeoMx spatial data using the BayesPrism. The output gene matrix is scaled, and I was wondering if there is anyway to use this data to perform DEG on specific cell populations' gene expression determined by the deconvolution process?

Below is a sample of the scaled data:

          DSP-1001660016227-D-A04.dcc DSP-1001660016227-D-A09.dcc DSP-1001660016227-D-A10.dcc
SAMD11                       3.1490931                   3.2087063                   4.8211229
ISG15                       -0.2266427                  -0.2266427                  -0.2266427
AGRN                        -0.2266427                  -0.2266427                  -0.2266427
DVL1                        -0.2266427                  -0.2266427                  -0.2266427
MXRA8                        3.1490931                   3.2087063                   3.0001598
ERRFI1                      -0.2266427                  -0.2266427                  -0.2266427
ENO1                         3.1490931                   3.2087063                   4.1266277
PGD                          3.1490931                  -0.2266427                  -0.2266427
PLOD1                        5.9765768                   5.4783866                   3.0001598
TNFRSF1B                    -0.2266427                  -0.2266427                  -0.2266427
GeoMx DifferentialExpression GeomxTools • 600 views
ADD COMMENT

Login before adding your answer.

Traffic: 667 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6