User: Jacob Michaelson

Reputation:
320
Status:
Trusted
Location:
Last seen:
13 years, 4 months ago
Joined:
14 years, 9 months ago
Email:
j********@comcast.net

Posts by Jacob Michaelson

<prev • 32 results • page 2 of 4 • next >
0
votes
4
answers
693
views
4
answers
GOstats and GenePix arrays
... Hi all, I'm trying to use the "guts" of the GOHyperG function in GOstats as a basis for a similar function for GenePix data. I've found a basic description of the phyper function in the context of GO: # How to implement phyper function for GO analysis # phyper(x-1, m, n-m , k, lower.tail = ...
go gostats written 13.4 years ago by Jacob Michaelson320
0
votes
0
answers
443
views
0
answers
background correction in marray
... Hi all, I'm working on some cDNA arrays and using maNorm() to normalize them . In the past I've used limma to do the normalization, as it includes a separate background-correcting function (just so I know exactly what is happening "under the hood"). I found a posting on the list that also noted th ...
normalization limma marray written 13.5 years ago by Jacob Michaelson320
0
votes
1
answer
569
views
1
answer
How does BioC map from Probe ID to Entrez Gene?
... Hi all, I've finished up with an analysis and in reviewing some of the annotations for gene symbols and RefSeqs, I've found some discrepancies that I don't know how to explain. The discrepancies are between Affy-supplied annotation (both both CSV and NetAffx) and BioC annotation. Let's take this ...
annotation go probe affy written 13.5 years ago by Jacob Michaelson320 • updated 13.5 years ago by John Zhang2.9k
0
votes
7
answers
465
views
7
answers
Answer: A: Thoughts on computer purchase
... > Most computer purchases here are through Dell, but I may be able to go > through HP if I wanted to get an AMD. > > > > Would there be a tremendous amount of difference in computing power for > things like Bioconductor and Genespring between, say > > > > Dual core ...
written 13.5 years ago by Jacob Michaelson320
0
votes
3
answers
591
views
3
answers
Comment: C: hgu133plus2 GO issues
... On Tue, 2006-04-18 at 09:37 -0700, Seth Falcon wrote: > Hi Jake, > > Jake writes: > > Could someone please help me understand the differences between the > > (hgu133plus2)GO, GO2PROBE, GO2ALLPROBES? I've found discepancies that I > > can't quite explain: > > > & ...
written 13.5 years ago by Jacob Michaelson320
0
votes
3
answers
591
views
3
answers
hgu133plus2 GO issues
... Hi list, Could someone please help me understand the differences between the (hgu133plus2)GO, GO2PROBE, GO2ALLPROBES? I've found discepancies that I can't quite explain: > mget("GO:0042611", hgu133plus2GO2PROBE) Error: value for 'GO:0042611' not found > mget("GO:0042611", hgu133plus2GO2AL ...
annotation go hgu133plus2 probe written 13.5 years ago by Jacob Michaelson320 • updated 13.5 years ago by James W. MacDonald51k
0
votes
0
answers
808
views
0
answers
repeated measures with limma+lme
... Hi all, I was wondering if I could get some constructive feedback on some code I'm using to analyze an Affymetrix repeated measures experiment. I've found through the list that limma's repeated measures capabilities are limited when it comes to specifying certain correlation structures, but I real ...
limma written 14.1 years ago by Jacob Michaelson320
0
votes
2
answers
350
views
2
answers
Answer: A: ANN: BioConductor website upgraded
... I think the site looks fantastic! Very modern, and I like the fact that the layout and style falls in line with many other open-source efforts. One suggestion: I have always found the workshop documentation (slides, exercises, etc.) to be very helpful, sometimes more so than the actual vignettes. ...
written 14.3 years ago by Jacob Michaelson320
0
votes
0
answers
400
views
0
answers
marray intensity normalization?
... Hi all, I'm a little more familiar with single-channel chips (Affy) than I am with spotted two-color arrays, and I'm now starting to get involved with the analysis of some two-color arrays. I was wondering (thinking of this from the single-channel mentality) if there's a way to use marray (or anot ...
marray convert written 14.3 years ago by Jacob Michaelson320
0
votes
3
answers
326
views
3
answers
misnamed annotation environments with annaffy
... Hi all, Several months ago I built a custom annotation package for Affy's Yeast 2.0 chip. Both I and the function I used gave some inconvenient names to the environments within the package and I've had some problems with annaffy because of it. My problem: An environment named "YEAST2GENENAMES" c ...
annotation annaffy written 14.4 years ago by Jacob Michaelson320 • updated 14.4 years ago by Seth Falcon7.4k

Latest awards to Jacob Michaelson

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 123 users visited in the last hour