[BioC] lumi and Affy bgadjust

[parantu shah]

Hi.

I am using Lumi package for analyzing Illumina gene expression array
data. I don't have control data and I am using sample probe
profile.txt file.

 I use 'force positive' and 'bgAdjust.affy' options to do background
correction. After doing VST and RSN normalization - estimate of differentially
expressed genes (using limma)  is very different (1675 vs. 1134).

I am attaching you the box plot of VST data after no correction,
forcepositive and bgAdjust.affy in a hope that it will be useful to
you in answering.

I would also appreciate any other suggestions you have.

Thanks and best regards,
Parantu.


--
Parantu Shah, PhD
Dept. of Biostatistics & Computational Biology
Dana-Farber Cancer Institute
Harvard School of Public Health

CLS-11075,  3 Blackfan Circle
Boston MA 02115
Phone : 617 582 8852
http://www.hsph.harvard.edu/~pshah



-- 
Parantu Shah, PhD
Dept. of Biostatistics & Computational Biology
Dana-Farber Cancer Institute
Harvard School of Public Health

CLS-11075,  3 Blackfan Circle
Boston MA 02115
Phone : 617 582 8852
http://www.hsph.harvard.edu/~pshah
-------------- next part --------------
A non-text attachment was scrubbed...
Name: bgcorr.pdf
Type: application/pdf
Size: 43203 bytes
Desc: not available
URL: <https://stat.ethz.ch/pipermail/bioconductor/attachments/20090921/15dd56c0/attachment.pdf>