1 Description

The rat2302frmavecs package was built from the set of 1023 microarray samples, distributed according to the table below. The maximum number of samples per dataset is 93, and was selected to have a uniform sample distribution across tissues (only 93 samples were available for the bone marrow tissue).

The table below reports the number of samples per dataset, for experiments conducted on rat4302 affymetrics platform. The 93 samples per dataset were selected as follow (steps applied for each dataset separately):

  1. The official metadata file (e.g.: E-GEOD-XXXX.sdrf.txt) was loaded, and filtered to keep only those samples associated to the correct microarray platform;

  2. A random uniform sampling (seed set to 4778) of 93 integer numbers (1 to number of samples of the dataset) were extracted

  3. The 93 rows of the metadata file were selected along with the corresponding samples;

  4. The 93 samples (.CEL files) were extracted from the RAW data zip archives from ArrayExpress repository;

  5. Once all 1023 (93 for each of the 11 tissues) samples were extracted the makeVectorPackage function was called with the parameter set to a vector of length 1023 (93 repetitions of each dataset names), and with annotation parameter set to rat2302cdf.

Step number 5 generates a package containing the vectors needed to the FRMA tool, affy ID based in case the annotation parameter was set to rat2302cdf.

Total Dataset Used
Adipose tissue 101 E-GEOD-13268 93
Brain 335 E-GEOD-28435 93
Eye 120 E-GEOD-5680 93
Heart 862 E-GEOD-57800 93
Kidney 1410 E-GEOD-57811 93
Liver 2218 E-GEOD-57815 93
Thigh muscle 158 E-GEOD-57816 93
Bone marrow 93 E-GEOD-63902 93
Mixed (testis/liver/brain/kidney) 264 E-MEXP-1568 93
Bronchus 164 E-TABM-458 93
Skeletal muscle 126 E-TABM-458 93
TOTAL 1023

2 Basic usage


celfile = system.file("extdata", "sample.CEL", package = "rat2302frmavecs")
affybatch = ReadAffy(filenames = celfile, cdfname = 'rat2302cdf')
eset = frma(affybatch)