Raw and subsetted soybean leaves iron-metabolism SummarizedExperiment

Source: R/data-se_soybean_ir_sub.R

This dataset contains raw RNA-sequencing read counts from a soybean dataset that compared leaves that were exposed to iron-rich (iron -postive) soil conditions versus leaves that were exposed to iron-poor (iron-negative) soil conditions. The data was collected 120 minutes after iron conditions were initiated. To save on size, this example dataset was generated by obtaining a random subset of 1 out of 10 genes from the original resource.

data(se_soybean_ir_sub)

Format

(1) A DelayedMatrix with 5,604 rows and 7 variables and 1 row per gene. Accessible by assay(se_soybean_ir_sub). (2) A List with 1 list element per treatment group combination and 1 row per gene. Accessible by rowData(se_soybean_ir_sub).

A data frame with 5,604 rows and 7 variables

Details

Raw and subsetted soybean leaves data SummarizedExperiment object

  • assay(se_soybean_ir_sub) Structure:

  • N.1 iron-negative condition replicate 1 raw read counts

  • N.2 iron-negative condition replicate 2 raw read counts

  • N.3 iron-negative condition replicate 3 raw read counts

  • P.1 iron-positive condition replicate 1 raw read counts

  • P.2 iron-positive condition replicate 2 raw read counts

  • P.3 iron-positive condition replicate 3 raw read counts

  • rowData(se_soybean_ir_sub) list element Structure:

  • ID gene name

  • logFC log fold change

  • logCPM log counts per million

  • LR likelihood ratio

  • PValue p-value

  • FDR FDR value

References

Moran Lauter AN, Graham MA. NCBI SRA bioproject accession: PRJNA318409.

See also

soybean_ir_sub and soybean_ir_sub_metrics