[BioC] applicability of tilingArray package

Michael Palumbo palumbo at wadsworth.org
Tue Nov 4 17:42:10 CET 2008


i have general questions regarding the applicability of the tilingArray 
package to my problem/data. i've used bioconductor in the past, but by 
no means am i an expert.

i have data from affy yeast tiling arrays - 3 mut and 3 wild type. i've 
run affy's TAS program on the CEL files - as a two sample analysis, ie, 
comparing wt to mut and viewed the results in IGB. my initial goal is to 
segment the results as was done in David et al, PNAS 2006. it seems to 
me there are fundamental differences in my data and the data of David et 
al. e.g., the normalization step described in tilingArray doc uses DNA 
hybridized to the chips as a reference - i don't have that, although i 
do have the wt data. a colleague thought i might be able to use the wt 
data in the normalization step, but that doesn't seem quite right to me. 
it is also described that normalization can occur by MM probes - maybe i 
can normalize the mut chip data w/ MM probes and completely ignore the 
wt data? i realize that if i did that, the result would no longer be a 
comparison of mut and wt and what i would 'see' would be different from 
what i currently see in IGB of the two sample TAS analysis. this also 
seems like it's not the best approach.

on the other hand, again, all i really want to do is segment the 
two-sample analysis that i've done. is there anything wrong with using 
the results of TAS's analysis? TAS does a normalization and has 
bandwidth averaging - as a non-expert, these are convenient and seem 
good to me.

thanks in advance for any and all responses/thoughts,
mike palumbo

Michael Palumbo					palumbo at wadsworth.org
Wadsworth Center				
Center for Medical Science
New York State Dept of Health
150 New Scotland Ave
Albany, NY 12208

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