[BioC] limma citations [was LimmaGUI for illumina data]

[Gordon Smyth]

>[BioC] LimmaGUI for illumina data
>Roy Williams royw at burnham.org
>Thu May 25 07:29:14 CEST 2006
>
>Hi,
>
>I have 2 questions:
>1. I would be really grateful to have a list of papers that cite limma -
>does such a list exist? If so could someone send it to me.

Dear Roy,

As far as I know, there's no such list, apart from what you can get 
from the usual sources (Web of Science, PubMed, Google Scholar etc). 
We don't spend our time making lists like this. The Web of Science 
lists 120 papers that cite the basic linear model paper Smyth (2004) 
which explains the eBayes stuff. Many papers using limma don't give a 
formal citation, unfortunately, so the number of published papers 
using limma is probably around a couple of hundred.

The Limma User's Guide has a section at the end listing a few of the 
early citers. Here's a few randomly chosen citers below from early this year.

Best wishes
Gordon

Stingl, J., Eirew, P., Ricketson, I., Shackleton, M., Vaillant, F., 
Choi, D., Li, H.I. and Eaves, C.J. (2006) Purification and unique 
properties of mammary epithelial stem cells. Nature, 439, 993-997.

Caruana, G., Cullen-McEwen, L., Nelson, A.L., Kostoulias, X., Woods, 
K., Gardiner, B., Davis, M.J., Taylor, D.F., Teasdale, R.D., 
Grimmond, S.M. et al. (2006) Spatial gene expression in the T-stage 
mouse metanephros. Gene Expr Patterns.

Dawson, P.A., Gardiner, B., Grimmond, S. and Markovich, D. (2006) 
Transcriptional profile reveals altered hepatic lipid and cholesterol 
metabolism in hyposulfatemic NaS1 null mice. Physiol Genomics.

Martinez, G., Georgas, K., Challen, G.A., Rumballe, B., Davis, M.J., 
Taylor, D., Teasdale, R.D., Grimmond, S.M. and Little, M.H. (2006) 
Definition and spatial annotation of the dynamic secretome during 
early kidney development. Dev Dyn.

Velazquez-Fernandez, D., Laurell, C., Saqui-Salces, M., Pantoja, 
J.P., Candanedo-Gonzalez, F., Reza-Albarran, A., Gamboa-Dominguez, A. 
and Herrera, M.F. (2006) Differential RNA Expression Profile by cDNA 
Microarray in Sporadic Primary Hyperparathyroidism (pHPT): Primary 
Parathyroid Hyperplasia versus Adenoma. World J Surg.



>2. I would like to use the limmaGUI or AffyLMGUI package with illumina
>array data (www.illumina.com). Is this possible? Could I load a .RData
>(or .lmn) data object which has just the column headers (experiments)
>and gene names along with the data? I have been using limma from the
>command line and it would help considerably to have a GUI which prints
>HTML reports.
>
>Many thanks for any advice you might be able to offer,
>
>Roy
>
>--
>Roy Williams PhD
>The Burnham Institute for Medical Research
>Bioinformatics Shared Resource
>Building 10 Offices 2405/6
>3010 Science Park Road
>San Diego, California
>92121 USA
>
>
>Tel: 858 646 3100 ext 3915
>email: royw at burnham.org
>web site: idmweb.burnham.org