diff --git a/Tutorial_HTM_2016.Rmd b/Tutorial_HTM_2016.Rmd index bd757bbf191087f25a02cee27c6f6200095c8190..c02b2cb5d9920d2ba0bbf06401bb19896cde226a 100755 --- a/Tutorial_HTM_2016.Rmd +++ b/Tutorial_HTM_2016.Rmd @@ -66,8 +66,8 @@ We first import the annotation of the plate. This consists of table that informs us about the content of every single well on the plate. ```{r import_annotation} -data_path <- "~/p12_data" -plate_map <- read.xlsx(xlsxFile = file.path(data_path, "plate_mapping.xlsx")) +data_path <- "~/embo_course_2014" +plate_map <- read.xlsx(xlsxFile = file.path("plate_mapping.xlsx")) head(plate_map) ``` @@ -88,7 +88,10 @@ by the machine learning algorithm, so we only extract this part of the file. ```{r readCellH5, dependson="plate_map", eval=FALSE} -path <- file.path(data_path, "_all_positions.ch5") +# path <- file.path(data_path, "Analysis_new/hdf5/_all_positions.ch5") +#path <- "~/embo_course_2014/Analysis_new/hdf5/_all_positions.ch5" + +path <- "/g/huber/course/htm_course_2016/embo_course_2014/Analysis_new/hdf5/_all_positions.ch5" c5f <- CellH5(path) c5_pos <- C5Positions(c5f, C5Plates(c5f)) predictions <- C5Predictions(c5f, c5_pos[[1]], mask = "primary__primary3", as = "name") diff --git a/plate_mapping.xlsx b/plate_mapping.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..b2186b4d41683b59b682d8b2f5b096c6e5e7c3d0 Binary files /dev/null and b/plate_mapping.xlsx differ