PGS Documentation

Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

The Create categorical attribute dialog allows us to create groups for a categorical attribute. By default, two groups are created, but additional groups can be added. 

  • Set Attribute name: to StateRename the groups Primed and NaiveExperimental Group
  • Select New Group twice to add two additional groups
  • Rename the groups Primed+shCTRL, Naive+shCTRL, Naive+shPOU5F1, and Naive+shNANOG
  • Drag and drop the samples from the Unassigned list to their groups as listed in the table below
Sample IDGroup Name
GSM2515899_200526580002_R01C01Primed+shCTRL
GSM2515900_200526580002_R02C01Primed+shCTRL
GSM2515901_200526580002_R03C01Naive+shCTRL
GSM2515902_200526580002_R04C01Naive+shCTRL
GSM2515903_200526580002_R05C01Naive+shPOU5F1
GSM2515904_200526580002_R06C01Naive+shPOU5F1
GSM2515905_200526580002_R07C01Naive+shNANOG
GSM2515906_200526580002_R08C01Naive+shNANOG

There should now be two four groups with two samples in each group (Figure 4).

...

Numbered figure captions
SubtitleTextAdding State attribute as a categorical group
AnchorNameState attribute

  • Select OK
  • Select Yes from the Add another categorical attribute dialog
  • Set Attribute name: to shRNA treatment
  • Select New Group to add an additional group
  • Rename the three groups ControlshPOU5F1, and shNANOG
  • Drag and drop the samples from the Unassigned list to their groups as listed in the table below
Sample IDGroup Name

GSM2515899_200526580002_R01C01

Control

GSM2515900_200526580002_R02C01

Control

GSM2515901_200526580002_R03C01

Control

GSM2515902_200526580002_R04C01

Control

GSM2515903_200526580002_R05C01

shPOU5F1

GSM2515904_200526580002_R06C01

shPOU5F1

GSM2515905_200526580002_R07C01

shNANOG

GSM2515906_200526580002_R08C01

shNANOG

There should now be three groups with samples in each group (Figure 5).

 

Numbered figure captions
SubtitleTextAdding shRNA treatment as a categorical attribute
AnchorNameAdding shRNA treatment

Image RemovedImage Removed

  • Select OK
  • Select No from the Add another categorical attribute dialog
  • Select Yes to save the spreadsheet

Two A new column as s been added to spreadsheet 1 (Differential Methylation Analysis) with the state and shRNA treatment of each sample (Figure 6). 

...