2024 August issues

[jashapiro]

Issues that came up during the August 2024 training

[jashapiro]

At

training-modules/intro-to-R-tidyverse/01-intro_to_base_R.Rmd

Line 341 in 8718d22

The output here is a logical vector telling us whether each value in example_vector is TRUE or FALSE

The variable is not named example_vector but should be renamed values_1_to_20

[jaclyn-taroni]

Let's keep track of the RRP items on this issue: AlexsLemonade/reproducible-research#184

[jaclyn-taroni]

01 bulk material.

We talk about the other QC report in bulk (i.e., the one not run via the script) as SRR585574, but if one links files as part of the setup, the other reports you get are for SRR585571.

There's also some ambiguity about how we talk about quality trimming since we don't quality trim and the 2020 paper we cite in the next paragraph mentions that trimming appears to have little effect.

The Salmon documentation notes that, given the way we run salmon quant, quantification may be more sensitive to calls that are likely to be erroneous (of low quality) and, therefore, quality trimming may be important.

We can no longer link to --validateMappings in the description of important options of the Salmon docs. However, where the link resolves does currently describe this flag in a note!

[jaclyn-taroni]

We had some issues in 02-gastric_cancer_tximeta with people running the following chunk twice:

training-modules/RNA-seq/02-gastric_cancer_tximeta.Rmd

Lines 125 to 129 in 8718d22

	```{r join-sample_meta_df}
	coldata <- coldata |>
	dplyr::inner_join(sample_meta_df, by = c("names" = "srr_accession"))
	coldata

If we rename what we are assigning to as something like coldata_joined and then we can do:

txi_data <- tximeta(coldata_joined)

[sjspielman]

The pathway analysis notebooks are still using an if statement to create directories. We should update them to use fs::dir_create().

[jashapiro]

We had some issues in 02-gastric_cancer_tximeta with people running the following chunk twice:

training-modules/RNA-seq/02-gastric_cancer_tximeta.Rmd

Lines 125 to 129 in 8718d22

	```{r join-sample_meta_df}
	coldata <- coldata |>
	dplyr::inner_join(sample_meta_df, by = c("names" = "srr_accession"))
	coldata

If we rename what we are assigning to as something like coldata_joined and then we can do:

txi_data <- tximeta(coldata_joined)

Similar potential issue in pathway analysis: Ora

[jaclyn-taroni]

We don't set a seed in the GSEA notebook, but perhaps we should.