From 00a4ed8afdb51e02ba2c8fd7be04e7812632f764 Mon Sep 17 00:00:00 2001 From: Emma Rand Date: Sun, 22 Oct 2023 15:15:14 +0100 Subject: [PATCH 1/2] correctfile location --- omics/week-5/workshop.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/omics/week-5/workshop.qmd b/omics/week-5/workshop.qmd index 164cf1d..8611348 100644 --- a/omics/week-5/workshop.qmd +++ b/omics/week-5/workshop.qmd @@ -95,16 +95,16 @@ We will carry out several steps We need to import both the normalised counts and the statistical results. We will need all of these for the visualisation and interpretation. -🎬 Import files saved from last week from the `results` folder: s30_normalised_counts.csv and s30_results.csv. I used the names `s30_count_norm` and `s30_results` for the dataframes. +🎬 Import files saved from last week from the `results` folder: S30_normalised_counts.csv and S30_results.csv. I used the names `s30_count_norm` and `s30_results` for the dataframes. ```{r} #| echo: false #---CODING ANSWER--- # Import the normalised counts -s30_count_norm <- read_csv("results/s30_normalised_counts.csv") +s30_count_norm <- read_csv("results/S30_normalised_counts.csv") # DE results -s30_results <- read_csv("omics/week-4/results/s30_results.csv") +s30_results <- read_csv("results/S30_results.csv") ``` From a4dbe2499ad5b3ed741da84917e005ca8d6a307f Mon Sep 17 00:00:00 2001 From: Emma Rand Date: Sun, 22 Oct 2023 15:17:29 +0100 Subject: [PATCH 2/2] path correction --- omics/week-5/workshop.qmd | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/omics/week-5/workshop.qmd b/omics/week-5/workshop.qmd index 8611348..be9ad31 100644 --- a/omics/week-5/workshop.qmd +++ b/omics/week-5/workshop.qmd @@ -209,7 +209,7 @@ s30_results_sig0.01 <- s30_results |> ```{r} # write to csv file write_csv(s30_results_sig0.01, - file = "omics/week-5/results/s30_results_sig0.01.csv") + file = "results/s30_results_sig0.01.csv") ``` ```{r} @@ -222,7 +222,7 @@ s30_results_sig0.05 <- s30_results |> ```{r} # write to csv file write_csv(s30_results_sig0.05, - file = "omics/week-5/results/s30_results_sig0.05.csv") + file = "results/s30_results_sig0.05.csv") ``` @@ -438,8 +438,8 @@ We will carry out several steps #| echo: false #---CODING ANSWER--- # import the normalised counts -prog <- read_csv("omics/week-5/data-raw/surfaceome_prog.csv") -hspc <- read_csv("omics/week-5/data-raw/surfaceome_hspc.csv") +prog <- read_csv("data-raw/surfaceome_prog.csv") +hspc <- read_csv("data-raw/surfaceome_hspc.csv") ``` @@ -456,7 +456,7 @@ prog_hspc <- bind_cols(prog, hspc[-1]) ```{r} # import the DE results -prog_hspc_results <- read_csv("omics/week-5/results/prog_hspc_results.csv") +prog_hspc_results <- read_csv("results/prog_hspc_results.csv") ``` @@ -568,7 +568,7 @@ prog_hspc_results_sig0.01 <- prog_hspc_results |> write to csv file ```{r} write_csv(prog_hspc_results_sig0.01, - file = "omics/week-5/results/prog_hspc_results_sig0.01.csv") + file = "results/prog_hspc_results_sig0.01.csv") ``` @@ -582,7 +582,7 @@ write to csv file ```{r} write_csv(prog_hspc_results_sig0.05, - file = "omics/week-5/results/prog_hspc_results_sig0.05.csv") + file = "results/prog_hspc_results_sig0.05.csv") ```