[BioC] Why some data missing when I use R to analysis the NimbleGen array

Benilton Carvalho beniltoncarvalho at gmail.com
Sat Jul 23 13:51:04 CEST 2011


this is not what I said. What I said was:

"If the NDF (or any other source) contains further information that
you want to use on the downstream analyses (for example, gene
associations or transcript IDs that you can link to probeset ID), then
you need to load the NDF manually, appropriately extract the bits of
information of interest and merge them with the preprocessed data."

It's *if* the NDF contained information that you find relevant, which
does not seem to be the case.

What you will need to do is to get the featureNames() of the output
object (after rma()) and map them to your units (transcript ID / gene
ID) of interest. One tool that will help you with this is BioMart (or
the R package biomaRt).

It also appears that you would benefit a lot from the help of a local
bioinformatics team, who should be able to assist you not only on the
analyses but also on the basic concepts and manipulation aspects of
microarray data.


On 23 July 2011 03:48, 陈娟 <gtzxchj at hotmail.com> wrote:
> Dear Professor,Thank you for your patience and kindness.I have thought that the NDF was loaded along with xys files using read.xysfiles(), or library(pd.090319.zea.kr.exptil) which was made based on the .ndf file and .xys files. But you meant that I should load it manually, and which command can achieve this ?I have searched the NDF and couldn't find the ID named like "GRMZM2G046829_T01"which are names in B73 genome. Instead, there are names like DESIGN_ID1, DESIGN_ID2 and other control probes. Do you know the reason that why the NDF excluded the B73 genome ID? In that case, how to find the corresponding ID of my interest?
> Truly YoursMaggie
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