dmd: Duchenne Muscular Dystrophy (DMD) Microarray Data Set

In lr98769/doppelgangerIdentifier: Identifies Doppelgangers Between Datasets With PPCC And Meta data

Duchenne Muscular Dystrophy (DMD) Microarray Data Set

Description

Unprocessed data set (no batch correction performed) formed from the combination of 2 independently-derived DMD data sets, Haslett et al. and Pescatori et al.

Usage

data(dmd)

Format

A data frame with 60 samples (columns) and 8813 ENSEMBL ID variables (rows):

Details

Both data sets were combined into a single data set with the following procedure:

1. All probes of both data sets were converted to ENSEMBL IDs using biomaRt.

2. To ensure a one-to-one mapping between the probes and ENSEMBL IDs in both data sets, all probes with no ENSEMBL ID were removed. Probes with multiple ENSEMBL IDs were replaced by the ENSEMBL ID with the smallest value (ENSEMBL IDs were ordered using the default order function and all ENSEMBL IDs after the first ENSEMBL ID was removed). We took the median values of probes sharing the same ENSEMBL ID. After this procedure, both data sets would consist of unique ENSEMBL ID variables.

3. To join both data sets without any null values or data imputation (since both data sets may not have the same number and type of ENSEMBL IDs), we took the intersection of ENSEMBL IDs between both data sets. This set of ENSEMBL IDs would be the ENSEMBL IDs of the joined data set.

4. Both data sets were joined along the shared set of ENSEMBL IDs.

References

Haslett JN, Sanoudou D, Kho AT, Bennett RR, Greenberg SA, Kohane IS, et al. Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle Proceedings of the National Academy of Sciences. 2002; 99:15000-5.

Pescatori M, Broccolini A, Minetti C, Bertini E, Bruno C, D'amico A, et al. Gene expression profiling in the early phases of DMD: a constant molecular signature characterizes DMD muscle from early postnatal life throughout disease progression The FASEB Journal. 2007; 21:1210-26.

lr98769/doppelgangerIdentifier documentation built on Aug. 2, 2022, 9:41 a.m.