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Michael Palumbo ▴ 50@michael-palumbo-2170
Last seen 7.1 years ago
hello, 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 IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.