[BioC] how to do time course data analysis of smd format?

Budhayash Gautam budhayashgautam at gmail.com
Tue Sep 14 12:03:34 CEST 2010

Hi all

i am working on some data obtained from smd database which is
basically a  time series data having human fibroblast infected by a
pathogen t. gondii . expression was recorded as follows

"a time course was performed during which RNA was purified from HFFs
that were mock- or parasite-infected for 1, 2, 4, 6, and 24 hpi with
T. gondii tachyzoites. To minimize host cell lysis following parasite
egress, the time course was limited to 24 h"

To perform differential expression on this data using limma i have to
build linear model or matrix.

how can i make matrix for this kind of data?
As i am new to bioconductor as well as microarray data analysis please
tell me if there is another way to do the analysis of this kind of

it would be useful if u kindly suggest articles, research papers or
tutorials on this .

with regards
Assistant Professor
Department Of Computational Biology And Bioinformatics,
Jacob School of Biotechnology & Bioengineering (JSBB)
Sam Higginbottom Institute of Agriculture, Technology and Sciences
(SHIATS)- Deemed University, Naini, Allahabad.
U.P. 211007

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