background probes for MTA in RASA · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

background probes for MTA in RASA

I need to make an analysis of expression of Mouse Transcriptome Arrays (MTA) from Affy. I've seen in the template for the "conf" file it needs a ".bgp" file with the information about the background probes with the variable name of "BackgroundProbeFile". Do you know if it's possible to download such kind of file from anywhere od do I have to generate it from scratch?

Thanks

microarrays affy mouse transcriptome-arrays rasa

• 1,840 views • link

updated 4.0 years ago by Ram

• written 10.8 years ago by Juan Cordero

0 answers

No answers yet.

Log in to answer this question.

More posts like this

How to compare the alignment to genome and transcriptome
written 7.0 years ago by Xiaokang •

I'm analysing RNA-Seq data of cod (Gadus morhua) which is a non-model species, meaning that the quality of its genome and annotation is not as …
Exclusion of miRNA microarray probes in PDX models
written 8.3 years ago by Juan Cordero

Hi, I would like to measure expression of miRNAs from (Affy) Clariom D arrays. cDNA comes from a PDX mouse model. Since extracting human genetic …
How to exclude probes from affy microarray before normalization?
written 9.4 years ago by Juan Cordero

Dear community, I have several Clariom D Human Arrays (Affymetrix) for which I want to remove some probes (the same set of probes in all …
Is it possible to run the GETHOGs algorithm on already computed pairs of orthologs from OMA?
written 9.7 years ago by Juan Cordero

Dear community, I've downloaded all pairs of orthologs (oma-pairs.txt file) from the OMA website and I wonder whether it is possible to find, for different …
Illumina cpg probe ID conversion to chromosomal location?
written 10.3 years ago by ahsan.raza.rana •

from where to get mouse 450K cpgmethylation annotation file Please guide me if any one having information related to this and what are gold standards …
Control probe sets in Affymetrix ST microarrays
written 10.7 years ago by Nathaniel •

I am analysing an Affymetrix Mouse Gene ST 2.0 array (http://www.affymetrix.com/catalog/131476/AFFY/Mouse+Gene+ST+Arrays) According to the annotation file available at the link above, the probesets consist of …
Affy Mouse Transcriptome Array analysis with Bioconductor
written 10.8 years ago by Juan Cordero

Dear community, I am a newbie in Affy analysis with Bioconcuctor and, while 3'UTR arrays analysis results quite straightforward (normalisation, DE, enrichment analysis...), I am …
Error: Circos Plot Creating In Windows Perl (First Time User Problem)
written 14.4 years ago by John •

<p>I am using the <a href="http://www.activestate.com/activeperl/downloads">activeperl</a> in my windows. I am trying to repeat a <a href="http://mkweb.bcgsc.ca/template/circos/tutorials/lessons/2d_tracks/histograms/configuration/">tutorial exercise</a> to make myself confidence that I can …
Measuring Microrna Expression On Affymetrix Gene St Chips
written 15.4 years ago by David Quigley

<p>We have recently started using the <strong>Affymetrix Human Gene ST 1.1</strong> and <strong>Mouse Gene 1.1 ST arrays</strong>. These arrays are designed primarily to measure expression …
Homology + Bioconductor
written 16.2 years ago by Mike Dewar

<p>After a few days (3? seems like longer) of trying to patch Bioconductor's <code>annotationTools</code> package I'm now giving up. The various annotation files I'm trying …