From 35ed1d67f7e5cc1ceeda20808c706e61fca2575a Mon Sep 17 00:00:00 2001 From: Zhiyu <zhiyu.zhao@utsouthwestern.edu> Date: Wed, 5 Aug 2020 00:04:34 -0500 Subject: [PATCH] V1.7.3 --- Change_Log.txt | 2 +- V1.7.3/ODA.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Change_Log.txt b/Change_Log.txt index 2cf4f0f..13308b0 100755 --- a/Change_Log.txt +++ b/Change_Log.txt @@ -1,6 +1,6 @@ ######################################################################### Change Log: -#v1.7.3, 06/18/2020: Library path was changed to ~/R_version/ODA. PCA labels and ellipses were added (not officially enabled yet). +#v1.7.3, 08/04/2020: R 4.0.2 was tested. Data template was changed to .xlsx. Macro was no longer needed. Library path was changed to ~/R/4.0.2-gccmkl for BioHPC. PCA labels and ellipses were added. Heatmap colors were added. #v1.7.2, 03/26/2020: A bug regarding empty feature IDs was fixed. #v1.7.1, 12/04/2019: Figures were saved as both .ps and .png files. Euler plot was disabled for >6 samples. Samples / features can be clustered or not on the heatmaps. #v1.7.0, 10/22/2019: Figures were saved as .ps files in a Figure folder. Correlation plot was genrated with the old method for better speed. Euler plot was disabled for >10 samples. Y axis of volcano plot could be raw or adjusted p-values. DESeq was renamed RLE as I would implement the DESeq differential expression analysis in the future. RLE is the same method used by DESeq but I slightly modified it to allow for zeros, missing values and / or values below the value filter. Due to this reason I couldn't use the DESeq normalization directly. diff --git a/V1.7.3/ODA.R b/V1.7.3/ODA.R index e8909de..86e3ed7 100755 --- a/V1.7.3/ODA.R +++ b/V1.7.3/ODA.R @@ -1,6 +1,6 @@ verNum='V1.7.3' #This script was developed by zhiyu.zhao@utsouthwestern.edu . -#v1.7.3, 08/04/2020: R 4.0.2 was tested. Data template was changed to .xlsx. Macro was no longer needed. Library path was changed to ~/R/ODA. PCA labels and ellipses were added. Heatmap colors were added. +#v1.7.3, 08/04/2020: R 4.0.2 was tested. Data template was changed to .xlsx. Macro was no longer needed. Library path was changed to ~/R/4.0.2-gccmkl for BioHPC. PCA labels and ellipses were added. Heatmap colors were added. #v1.7.2, 03/26/2020: A bug regarding empty feature IDs was fixed. #v1.7.1, 12/04/2019: Figures were saved as both .ps and .png files. Euler plot was disabled for >6 samples. Samples / features can be clustered or not on the heatmaps. #v1.7.0, 10/22/2019: Figures were saved as .ps files in a Figure folder. Correlation plot was generated with the old method for better speed. Euler plot was disabled for >10 samples. Y axis of volcano plot could be raw or adjusted p-values. DESeq was renamed RLE as I would implement the DESeq differential expression analysis in the future. RLE is the same method used by DESeq but I slightly modified it to allow for zeros, missing values and / or values below the value filter. Due to this reason I couldn't use the DESeq normalization directly. -- GitLab