Hey,
The Pasilla data comes as a data package in Bioconductor, called pasilla. The expression data and metadata come 'shipped' / 'bundled' with the package via the 'extdata' directory. You should be able to obtain them like this:
1, install and load package
if (!requireNamespace('BiocManager', quietly = TRUE))
install.packages('BiocManager')
BiocManager::install('pasilla')
library('pasilla')
2, retrieve and prepare the data
pasCts <- system.file('extdata', 'pasilla_gene_counts.tsv',
package='pasilla', mustWork=TRUE)
pasAnno <- system.file('extdata', 'pasilla_sample_annotation.csv',
package='pasilla', mustWork=TRUE)
cts <- as.matrix(read.csv(pasCts,sep='\t',row.names='gene_id'))
coldata <- read.csv(pasAnno, row.names=1)
coldata <- coldata[,c('condition','type')]
rownames(coldata) <- sub('fb', '', rownames(coldata))
cts <- cts[, rownames(coldata)]
coldata
condition type
treated1 treated single-read
treated2 treated paired-end
treated3 treated paired-end
untreated1 untreated single-read
untreated2 untreated single-read
untreated3 untreated paired-end
untreated4 untreated paired-end
cts[1:5,1:5]
treated1 treated2 treated3 untreated1 untreated2
FBgn0000003 0 0 1 0 0
FBgn0000008 140 88 70 92 161
FBgn0000014 4 0 0 5 1
FBgn0000015 1 0 0 0 2
FBgn0000017 6205 3072 3334 4664 8714
You can then process that in EdgeR or DESeq2.
-------------
The limma / EdgeR authors list other supplementary data here:
If, however, you specifically mean the targets.txt file from the f1000 workflow, From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline, then it's stated that this file is not available publicly:
Except for the targets file targets.txt, all data analyzed in the
workflow is read automatically from public websites
You can easily create it though.
Kevin