User: Isaac Neuhaus

gravatar for Isaac Neuhaus
Isaac Neuhaus360
Reputation:
360
Status:
Trusted
Location:
United States
Last seen:
2 years, 5 months ago
Joined:
15 years, 6 months ago
Email:
i************@bms.com

Posts by Isaac Neuhaus

<prev • 36 results • page 1 of 4 • next >
0
votes
1
answers
666
views
1
answers
Comment: C: AnnotationDbi packages missing in current release
... Yes. Thank you. ...
written 2.4 years ago by Isaac Neuhaus360
0
votes
1
answers
666
views
1
answers
Answer: A: AnnotationDbi packages missing in current release
... My bad. I figure that I needed to load a couple of libraries before I run makeDBPackage. Here is the procedure: library(AnnotationForge) library(org.Rn.eg.db) library(rat.db0) makeDBPackage("RATCHIP_DB", affy = TRUE, prefix="htrat230pm", fileName="HT_Rat230_PM.na35.annot.1.csv", baseMapType="gbNRe ...
written 2.4 years ago by Isaac Neuhaus360 • updated 2.4 years ago by James W. MacDonald45k
4
votes
1
answer
666
views
1
answer
AnnotationDbi packages missing in current release
... The following packages are missing in the current version of Bioiconductor (R): htmg430b.db,  primeview.db, htrat230pm.db, hthgu133pluspm.db, htmg430a.db, htmg430pm.db. Is there any way I can create them. I tried using the AnnotationForge package but I was not able to build them with the Affymetrix ...
0
votes
0
answers
580
views
0
answers
Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
... Lei Huang [guest] writes: > > > Dear all, > > I am working on a set of Affymetrix GeneChip miRNA 4.0 microarray data and would like to perform > differential expression analysis using Bioconductor packages. Since this is a fairly new platform, no > CDF and annotation packages ...
mirna annotation cdf makecdfenv written 3.8 years ago by Isaac Neuhaus360
0
votes
2
answers
303
views
2
answers
Comment: C: matchprobes vignette?
... I have installed R version 1.9 (64 bit compiled) and the Biocunductor packages release 1.4 which include the vsn package 1.4.13 and I am getting the following error: data <- ReadAffy(filenames=cels, sampleNames=names, verbose=F) > vsn.data <- expresso(data, normalize.method="vsn", bg.corr ...
written 13.4 years ago by Isaac Neuhaus360
0
votes
1
answers
248
views
1
answers
Answer: A: limma posterior variance
... Does anybody know how to set up the proxy in R to be able to use the getBioC() function and install the Bioconductor packages? Thanks. Isaac ...
written 13.5 years ago by Isaac Neuhaus360
0
votes
2
answers
418
views
2
answers
Answer: A: vsn procedure error
... You have to add the following line before you can use vsn as a normalization method. normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") Isaac Edmund Chang wrote: > Hi all, > I'm trying out the vsn procedure instead of rma. But i got the > following error message. W ...
written 13.5 years ago by Isaac Neuhaus360
0
votes
4
answers
336
views
4
answers
Comment: C: P calls (VSN and RMA)
... Wolfgang: For the VSN and RMA we used only the PMvalues with the affy version 1.2.25. raw.data <- ReadAffy(filenames=cels, sampleNames=names, verbose=F) vsn.data <- expresso(raw.data, normalize.method="vsn", bg.correct=F, pmcorrect.method="pmonly", summary.method="medianpolish") rma.data < ...
written 13.9 years ago by Isaac Neuhaus360
0
votes
4
answers
336
views
4
answers
P calls (VSN and RMA)
... We agree with Rafael that using algorithms such as VSN and RMA greatly reduces the noise at the lower intensities (hurray!). However, there is still the biological fact that a lot of the probesets on any chip assay genes that are not expressed in the cell type being tested. Incorporating the null me ...
affy vsn written 13.9 years ago by Isaac Neuhaus360 • updated 13.9 years ago by Petra B Ross-MacDonald20
0
votes
1
answers
463
views
1
answers
Comment: C: Simple questions about p values adjustment in limma/multt est
... We have a loan SGI Altix system runing linux with the IA-64 chip. I was wondering if anybody has compiled R in such a system as well as the Bioconductor packages ...
written 14.3 years ago by Isaac Neuhaus360

Latest awards to Isaac Neuhaus

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 2.2.0
Traffic: 395 users visited in the last hour