Question: Does bioconductor now has microarray cross-platform merging and normalization methods?
0
gravatar for Shi-Xiang Wang
15 months ago by
China/Shanghai/ShanghaiTech. University
Shi-Xiang Wang0 wrote:

I see many packages about cross-platform merging and normalization methods have been removed, such as inSilico Merging
, VirtualArray and so on. Does bioconductor now have such package?

microarray software error • 382 views
ADD COMMENTlink modified 15 months ago by Steve Lianoglou12k • written 15 months ago by Shi-Xiang Wang0
Answer: Does bioconductor now has microarray cross-platform merging and normalization me
0
gravatar for Steve Lianoglou
15 months ago by
Denali
Steve Lianoglou12k wrote:

You haven't said what you would want to do the cross-platform merging for, but I think you're going down the wrong rabbit hole.

Often times people inquire about merging different platforms so that they can combine different studies that are about "the same thing" and increase their N. If this is what you are trying to do, you will be better served trying a meta analysis, which is to say that you analyze each dataset individually but more formally look at concordance of results across the separate studies.

You could look at the GeneMeta or crossmeta packages for some examples.

Some threads on this support site about similar questions:

Merge different datasets regarding a common number of DE genes in R

how to merge affy and agilent array

 

ADD COMMENTlink written 15 months ago by Steve Lianoglou12k
Thanks. 在 2017年12月22日 03:00, Steve Lianoglou [bioc] 写道: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User Steve Lianoglou <https: support.bioconductor.org="" u="" 2771=""/> wrote > Answer: Does bioconductor now has microarray cross-platform merging > and normalization methods? > <https: support.bioconductor.org="" p="" 104426="" #104440="">: > > You haven't said what you would want to do the cross-platform merging > for, but I think you're going down the wrong rabbit hole. > > Often times people inquire about merging different platforms so that > they can combine different studies that are about "the same thing" and > increase their N. If this is what you are trying to do, you will be > better served trying a meta analysis, which is to say that you analyze > each dataset individually but more formally look at concordance of > results across the separate studies. > > You could look at the GeneMeta > <http: bioconductor.org="" packages="" release="" bioc="" html="" genemeta.html=""> or > crossmeta > <http: bioconductor.org="" packages="" release="" bioc="" html="" crossmeta.html=""> > packages for some examples. > > Some threads on this support site about similar questions: > > Merge different datasets regarding a common number of DE genes in R > <https: support.bioconductor.org="" p="" 65506=""/> > > how to merge affy and agilent array > <https: support.bioconductor.org="" p="" 71972=""/> > > ------------------------------------------------------------------------ > > Post tags: software error, microarray > > You may reply via email or visit > A: Does bioconductor now has microarray cross-platform merging and normalization me >
ADD REPLYlink written 15 months ago by Shi-Xiang Wang0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 155 users visited in the last hour