From 425f967372b1b2c82489a0e6e0f94dd451066463 Mon Sep 17 00:00:00 2001 From: jakebeal Date: Wed, 27 Sep 2017 14:34:57 -0500 Subject: [PATCH 1/4] placeholders no longer needed now that directories automatically self-create --- template_analysis/plots/placeholder.txt | 1 - template_colormodel/plots/placeholder.txt | 1 - 2 files changed, 2 deletions(-) delete mode 100644 template_analysis/plots/placeholder.txt delete mode 100644 template_colormodel/plots/placeholder.txt diff --git a/template_analysis/plots/placeholder.txt b/template_analysis/plots/placeholder.txt deleted file mode 100644 index 152f67e..0000000 --- a/template_analysis/plots/placeholder.txt +++ /dev/null @@ -1 +0,0 @@ -A placeholder to make sure the plots directory is here when checked out diff --git a/template_colormodel/plots/placeholder.txt b/template_colormodel/plots/placeholder.txt deleted file mode 100644 index 152f67e..0000000 --- a/template_colormodel/plots/placeholder.txt +++ /dev/null @@ -1 +0,0 @@ -A placeholder to make sure the plots directory is here when checked out From ef870c1f7ceb015f0d5c533a5ef3e008296342b7 Mon Sep 17 00:00:00 2001 From: jakebeal Date: Wed, 27 Sep 2017 14:37:29 -0500 Subject: [PATCH 2/4] note that for a single channel, color control is optional --- template_colormodel/make_color_model.m | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/template_colormodel/make_color_model.m b/template_colormodel/make_color_model.m index b497c06..7ba9d2c 100644 --- a/template_colormodel/make_color_model.m +++ b/template_colormodel/make_color_model.m @@ -25,7 +25,7 @@ channels{1} = Channel('FITC-A', 488, 515, 20); channels{1} = setPrintName(channels{1}, 'EYFP'); % Name to print on charts channels{1} = setLineSpec(channels{1}, 'y'); % Color for lines, when needed -colorfiles{1} = [stem0312 'EYFP_P3.fcs']; +colorfiles{1} = [stem0312 'EYFP_P3.fcs']; % If there is only one channel, the color file is optional channels{2} = Channel('PE-Tx-Red-YG-A', 561, 610, 20); channels{2} = setPrintName(channels{2}, 'mKate'); From 16b14d156c881cb3dcea160bcb106a7956d38039 Mon Sep 17 00:00:00 2001 From: jakebeal Date: Fri, 29 Sep 2017 07:20:29 -0500 Subject: [PATCH 3/4] Add note about when to change AP number of Gaussian components --- template_analysis/batch_template.m | 3 +++ template_analysis/plusminus_template.m | 3 +++ template_analysis/transfercurve_template.m | 3 +++ 3 files changed, 9 insertions(+) diff --git a/template_analysis/batch_template.m b/template_analysis/batch_template.m index 4141276..f0880e9 100644 --- a/template_analysis/batch_template.m +++ b/template_analysis/batch_template.m @@ -19,6 +19,9 @@ AP=setPemDropThreshold(AP,5'); % Add autofluorescence back in after removing for compensation? AP=setUseAutoFluorescence(AP,false'); +% By default, analysis tries to fit constitutive to “transformed” and “non-transformed” components +% If your distribution is more complex or less complex, you can change the number of components +% AP=setNumGaussianComponents(AP,3); % Make a map of condition names to file sets stem1011 = '../example_assay/LacI-CAGop_'; diff --git a/template_analysis/plusminus_template.m b/template_analysis/plusminus_template.m index 8d0ce1a..df7aa8b 100755 --- a/template_analysis/plusminus_template.m +++ b/template_analysis/plusminus_template.m @@ -23,6 +23,9 @@ AP=setPemDropThreshold(AP,5'); % Add autofluorescence back in after removing for compensation? AP=setUseAutoFluorescence(AP,false'); +% By default, analysis tries to fit constitutive to “transformed” and “non-transformed” components +% If your distribution is more complex or less complex, you can change the number of components +% AP=setNumGaussianComponents(AP,3); % Make a map of the batches of plus/minus comparisons to test % This analysis supports two variables: a +/- variable and a "tuning" variable diff --git a/template_analysis/transfercurve_template.m b/template_analysis/transfercurve_template.m index cd32c96..f63be3b 100644 --- a/template_analysis/transfercurve_template.m +++ b/template_analysis/transfercurve_template.m @@ -25,6 +25,9 @@ AP=setPemDropThreshold(AP,5'); % Add autofluorescence back in after removing for compensation? AP=setUseAutoFluorescence(AP,false'); +% By default, analysis tries to fit constitutive to “transformed” and “non-transformed” components +% If your distribution is more complex or less complex, you can change the number of components +% AP=setNumGaussianComponents(AP,3); % Make a map of induction levels to file sets stem1011 = '../example_assay/LacI-CAGop_'; From 4d963014268d4dac120164732c3de48b7536ab64 Mon Sep 17 00:00:00 2001 From: jakebeal Date: Sat, 14 Oct 2017 06:10:59 -0500 Subject: [PATCH 4/4] correct typo --- template_analysis/batch_template.m | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/template_analysis/batch_template.m b/template_analysis/batch_template.m index f0880e9..689e265 100644 --- a/template_analysis/batch_template.m +++ b/template_analysis/batch_template.m @@ -19,7 +19,7 @@ AP=setPemDropThreshold(AP,5'); % Add autofluorescence back in after removing for compensation? AP=setUseAutoFluorescence(AP,false'); -% By default, analysis tries to fit constitutive to “transformed” and “non-transformed” components +% By default, analysis tries to fit constitutive to transformed and non-transformed components % If your distribution is more complex or less complex, you can change the number of components % AP=setNumGaussianComponents(AP,3);