User: Nathaniel

gravatar for Nathaniel
Nathaniel20
Reputation:
20
Status:
New User
Location:
Denmark
Last seen:
3 years, 11 months ago
Joined:
3 years, 11 months ago
Email:
r****************@gmail.com

Posts by Nathaniel

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
971
views
1
answer
PLIER normalization for Affymetrix GeneChip arrays?
... The two most common normalization methods for the old Affymetrix 3’ GeneChips are RMA and PLIER. I have been reading about PLIER in the following reference http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2623311/, and it states that it requires a Perfect Match and Missmatch probess. However, thew new A ...
microarray normalization oligo affymetrix rma written 4.0 years ago by Nathaniel20 • updated 4.0 years ago by James W. MacDonald51k
2
votes
1
answer
799
views
1
answer
what is fitProbeLevelModel()? doing
... I am doing a quality control for an Affymetrix Mouse Gene ST 2.0 microarray using RMA method. As far as I understand, this method performs a background correction, log2 transformation and then a quantile normalization. This ensures that the distribution of intensities between different microarrays i ...
microarray oligo affymetrix written 4.0 years ago by Nathaniel20 • updated 4.0 years ago by James W. MacDonald51k
0
votes
2
answers
1.8k
views
2
answers
Comment: C: what is the difference between "pd.mogene.2.0.st" and "mogene20sttranscriptclust
... That perfectly answers my question, thanks James! ...
written 4.0 years ago by Nathaniel20
0
votes
2
answers
1.8k
views
2
answers
Comment: C: what is the difference between "pd.mogene.2.0.st" and "mogene20sttranscriptclust
... Excellent answer James, thanks a lot! just a final question: when mapping the 'core' probesets to genes using mogene20sttranscriptcluster.db package, should I expect to have duplicated genes in the collapsed matrix, or ALL probesets mapping to the same gene will have been collapsed? I expected to ...
written 4.0 years ago by Nathaniel20
0
votes
2
answers
1.8k
views
2
answers
6
votes
2
answers
1.8k
views
2
answers
what is the difference between "pd.mogene.2.0.st" and "mogene20sttranscriptcluster.db"?
... I am trying to annotate transcripts from an Affymetrix Mouse Gene ST 2.0 microarray using 'oligo', but I have found so many resources and annotation approaches that I cannot figure out the relationships and differences between them. So, to start with, what is the difference between the packages pd. ...
affymetrix mouse gene arrays written 4.0 years ago by Nathaniel20
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Load CDF files for Affymetrix ST 2.0 microarrays
... Thanks a lot for the answer Guido. after some googling I realized that someone had already made the CDF files to work with 'oligo': https://bioconductor.org/packages/release/data/annotation/html/pd.mogene.2.0.st.html Thus, I performed the analysis as follows: library(oligo) # Load the CEL files ...
written 4.0 years ago by Nathaniel20
0
votes
1
answer
1.4k
views
1
answer
Load CDF files for Affymetrix ST 2.0 microarrays
... I am analysing an Affymetrix Mogene 2.0 ST array, and I would like to collapse all cross-hybridizing probesets into a single transcript cluster. That is, reduce all rows with probesets mapping to different transcripts to a single row. A first approach I thought was to annotate all probesets with th ...
microarray customcdf cdf oligo written 4.0 years ago by Nathaniel20 • updated 4.0 years ago by Guido Hooiveld2.5k

Latest awards to Nathaniel

Popular Question 4.0 years ago, created a question with more than 1,000 views. For Load CDF files for Affymetrix ST 2.0 microarrays

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 294 users visited in the last hour