2009/6/23 Alberto Goldoni <alberto.goldoni1975@gmail.com>

> Try to use rankProd package contains functions for the analysis of gene
> expression microarray data, in
> particular the identi cation of di erentially expressed genes. RankProd
> utilizes the so called rank
> product non-parametric method (Breitling et al., 2004, FEBS Letters 573:83)
> to identify up-regulated
> or down-regulated genes under one condition against another condition, e.g.
> two di erent treatments,
> two di erent tissue types, etc.It is indicated for "Multiple origins".
> Follow the vignette.
>
> Best regards.
>
> 2009/6/23 Hui Yu <sheen2006@gmail.com>
>
> In my opinion, you should normalize, at least with regard to the two
>> different platforms, before attempting to merge duplicated
>> measurements of identical samples. Most probabably you'll end up
>> averaging the measurements of the duplicatedly-measured probes, and
>> collating the measurements for different genes from different
>> platforms into one single data column. These operations require you
>> ensure that the measurements from the two separate platforms are
>> comparable by the time of merging.
>> You may want to normalize only the platform-specific bias before the
>> merging; a loess-like calibration based on the 168*50*2 data-points
>> may suffice for this purpose. You have 168*50 pairs of data-points,
>> where each pair of data-points, one from GPL3694 and the other from
>> GPL3696, should be theoretically identical. A loess regression will
>> suppress the artificial difference between GPL3696 and GPL3694.
>> After the merging, which resulted in 50 data-columns each
>> corresponding to a different sample, you can implement whatever
>> normalization that came up to your mind in ordinary cases. Given the
>> fact that you have only ~5000 probes on each chip, which account for
>> only 25% of the total number of human genes, however, it may be
>> riskful to apply any global normalization that is based on the
>> 'invariable-total-expression' assumption. Maybe you need addtional
>> information to normalize between samples.
>> Any other opinions?
>>
>> On Fri, Jun 19, 2009 at 10:06 AM, LiGang<luzifer.li@gmail.com> wrote:
>> > Dear list,
>> >
>> > I have one question about merging (Combining) microarray datasets.
>> >
>> > I have 50 samples, and each sample was hybridized to 2 different
>> platforms---
>> > GPL3694 (5352 probes) and GPL3696 (also 5352 probes) in duplicate.
>> > There were 168 probes identical between these two platforms.
>> >
>> > I want to merge (combine) two hybridization files of each sample before
>> > performing normalization for all 50 samples.
>> > What appropriate method can be used to do this?
>> > Can the common 168 probes provide some information?
>> >
>> > Thanks!
>> > ---
>> > LiGang
>> >
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>> >
>>
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>
>
>
> --
> -----------------------------------------------------
> Dr. Alberto Goldoni
> Bologna, Italy
> -----------------------------------------------------
>



-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Bologna, Italy
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