[xps]Analysis of Affymetrix Clarion S array using xps package
1
0
Entering edit mode
snj • 0
@snj-12326
Last seen 7.1 years ago

Hi all,

 

I would like to analyze the data obtained with Affymetrix's new Clariom S arrays using xps package.

Now, I am trying to make a scheme file for Clarion S Mouse array using import.exon.scheme().

However, it simply does not work because Affymetrix has changed the format of transcript and probe set information.

Could anyone make a scheme file for Affymetrix's Clarion array?

xps • 1.5k views
ADD COMMENT
1
Entering edit mode
cstrato ★ 3.9k
@cstrato-908
Last seen 5.5 years ago
Austria

Hi,

Please note that HTA-2.0, MTA-1.0 and RTA-1.0 arrays are not supported by 'xps', see:
https://stat.ethz.ch/pipermail/bioconductor/2014-March/058538.html

Regards,
Christian

ADD COMMENT
0
Entering edit mode

Thank you, Christian.

I understood the situation.

 

I have tried to constuct transctipt.csv and probeset.csv from the NetAffx's annotation files.

Some differences were modificated, but NetAffx's transcript annotation file does not contain AFFX control information.

Such information is included in .pgf file. However, my code skill is poor, it takes much time to prepare that files.

I gave up to use xps package and have performed rma normalizaion using oligo package.

ADD REPLY

Login before adding your answer.

Traffic: 558 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6