[BioC] (no subject)

Joern Toedling toedling at ebi.ac.uk
Fri Nov 2 17:56:42 CET 2007


the package ALL contains the combined samples from two studies.
Patients with T-cell (n=33) and B-cell (n=95) were analyzed separately,
and published in those two papers:

4.    Sabina Chiaretti, Xiaochun Li, Robert Gentleman, Antonella
Vitale, Kathy S. Wang, Franco Mandelli, Robin Foa,  Jerome Ritz. Gene
Expression Profiles of B-lineage Adult Acute Lymphocytic Leukemia Reveal
Distinct Genetic Patterns that Identify Lineage and Distinct Mechanisms
of Transformation. Clinical Cancer Research, 2005, 11(20):7209-19.

9.    Sabina Chiaretti, Xiaochun Li, Robert Gentleman, Antonella
Vitale, Marco Vignetti, Franco Mandelli, Jerome Ritz, Robin Foa. (2004)
Gene Expression Profile of Adult T-Cell Acute Lymphocytic Leukemia
Identifies Distinct Subsets of Patients with Different Response to
Therapy and Survival (Blood, 1 April 2004, Vol. 103, No. 7)

Whether it is B- or T-cell leukemia and the stage of the disease is
indicated in the phenoData column "BT".

> table(ALL$BT)

 B B1 B2 B3 B4  T T1 T2 T3 T4
 5 19 36 23 12  5  1 15 10  2

See the extensive manual page (?ALL) of the data set for a more detailed
Note that the package ALL only contains the RMA-preprocessed data. There
may be a second data package containing the raw CEL files of this data
set soon.


Thomas Elliott wrote:
> Hi,
> I'm confused about the nature of the data used in the ALL example in  
> Bioconductor.  The paper (Chiaretti et al 2004) describes a study of  
> T-cell ALL and doesn't mention BCR-ABL, while the Bioconductor  
> example (e.g. in the Genome Biology paper) works through a comparison  
> of BCR/ABL v. ALL1/AF4, which are, I think, markers for B-ALL.  I  
> can't find anything in the phenoData which describes which patients  
> have T-ALL or B-ALL.
> Thanks.
> Tom Elliott
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