Generation of per_well table

Hello,
I would like to prepare some column diagramms (for example median values with standard deviation) showing per well data. In the experiment I did siRNA silencing in triplicates and we took 20 images per well. During the CellProfiler measurement the mean, median values as well as SD were calculated on the per image level. Is it somehow possible to cumulate the data from the well repilcates and show them on a diagramm in CPA? Or can I create a table with median, mean values of the single wells?
Thank in advance.
Best,
Gergo

HI Gergo,

One way to depict this easily in CPA is through the PlateViewer tool. There, you can visualize per-image data aggregated on a per-well basis, using the mean, median, std among others.

Another option is to use a grouping field in the properties file. Below is the relevant annotation describing how to do this.

[code]# ==== Dynamic Groups ====

Here you can define groupings to choose from when classifier scores your experiment. (eg: per-well)

This is OPTIONAL, you may leave "groups = ".

FORMAT:

group_XXX = MySQL select statement that returns image-keys and group-keys. This will be associated with the group name “XXX” from above.

EXAMPLE GROUPS:

groups = Well, Gene, Well+Gene,

group_SQL_Well = SELECT Per_Image_Table.TableNumber, Per_Image_Table.ImageNumber, Per_Image_Table.well FROM Per_Image_Table

group_SQL_Gene = SELECT Per_Image_Table.TableNumber, Per_Image_Table.ImageNumber, Well_ID_Table.gene FROM Per_Image_Table, Well_ID_Table WHERE Per_Image_Table.well=Well_ID_Table.well

group_SQL_Well+Gene = SELECT Per_Image_Table.TableNumber, Per_Image_Table.ImageNumber, Well_ID_Table.well, Well_ID_Table.gene FROM Per_Image_Table, Well_ID_Table WHERE Per_Image_Table.well=Well_ID_Table.well[/code]Then, in CPA, using the Boxplot visualization tool, you can select the well group XXX that you created under “Group x-axis by”.

Regards,
-Mark

Hi Mark,

Coming back to the question asked a while ago by Gergo … you did recommend using PlateViewer which is indeed a very nice module.

Is there any way that one can copy/save the data shown in the PlateViewer module as a table … ie represented as columns vs rows? This will be great function!

This is also valid for the other modules of the CPA (Boxplot, Histogram, ScatterPlot) … It will great to be able to show/copy/save a table with the data plotted on the graphs.

Thanks,

Dan

[quote=“Dan_Erix”]Is there any way that one can copy/save the data shown in the PlateViewer module as a table … ie represented as columns vs rows? This will be great function!
[snip]
This is also valid for the other modules of the CPA (Boxplot, Histogram, ScatterPlot) … It will great to be able to show/copy/save a table with the data plotted on the graphs.[/quote]

Unfortunately, CPA does not support this functionality for either of these items.
-Mark