User: Martha Behnke

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Martha Behnke100
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Posts by Martha Behnke

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Comment: C: affxparser updateCelUnit question
... Thank you very much! I have successfully written the data out, now I'm checking to make sure it went to the right places :) I really appreciate your quick help!! On Wed, Jul 13, 2011 at 2:44 PM, Henrik Bengtsson wrote: > Hi. > > On Wed, Jul 13, 2011 at 10:49 AM, M Behnke wrote: > & ...
written 8.1 years ago by Martha Behnke100
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Answer: A: affxparser updateCelUnit question
... This works -- at least it runs without error. I will do a few and make sure the data looks like data when I read it back in. thank you very much!! On Wed, Jul 13, 2011 at 2:21 PM, Harris A. Jaffee wrote: > Your idxs seems to be of type character when it ought to be numeric, > at least w ...
written 8.1 years ago by Martha Behnke100
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Answer: A: affxparser updateCelUnit question
... Hi, Thanks for the reply! I didn't think I could use updateCel since I only have the 247,899 PM values. I did try it though and something strange is happening: With this code: files=list.files(pattern="[.](CEL)$") names=colnames(normed.1) pathname <- file.path(getwd(), basename(files[1])) int ...
written 8.1 years ago by Martha Behnke100
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Answer: A: affxparser updateCelUnit question
... Oh, thank you! I thought I had solved the CDF problem when I figured out that this package requires a copy of the CDF file to be in the working directory, because the CDF-specific error messages went away. I can now get it to find my cdf file but still doesn't like it, but I will go away and Googl ...
written 8.1 years ago by Martha Behnke100
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affxparser updateCelUnit question
... Hello all, I have normalized data from hgu133a2 microarray experiments using a custom algorithm, in the format of a matrix with rowname=probe position and columns the normalized intensity values for each sample (125 samples). I am trying to write the data back out to individual CEL files using affx ...
microarray hgu133a2 affxparser written 8.1 years ago by Martha Behnke100
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Having trouble with new brainarray CDF
... My apologies, the subject line and discussion were about the brainarray CDFs and the fact that they were now updated, and my problem is with the updates so the background seemed appropriate. I've changed the subject line now. Thank you for responding so quickly, however, using the code you suggest ...
microarray annotation annotationdata affymetrixchip hgu133a2 cdf probe graph annotationdbi written 8.3 years ago by Martha Behnke100 • updated 8.3 years ago by Marc Carlson7.2k
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BrainArray custom CDF repository missing in biocReposList()
... Hello group, Has anyone tried to use the updated brainarray files? I have searched the mail lists and this is the most recent thread regarding them, and I found no mention of changes in usage anywhere. I updated to v14.1.0 for hgu133a2hsrefseq and it loads properly: > library(hgu133a2hsrefseq ...
microarray cdf probe graph written 8.3 years ago by Martha Behnke100 • updated 8.3 years ago by James W. MacDonald50k
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Answer: A: can't get limma for R 2.12.0 x64?
... I had the same problem but was too busy to pursue it at the time - I'm interested in the response too! Martha Sent from my Verizon Wireless BlackBerry -----Original Message----- From: Jenny Drnevich Sender: bioconductor-bounces at stat.math.ethz.ch Date: Tue, 09 Nov 2010 15:15:39 To: Subject: [B ...
written 8.8 years ago by Martha Behnke100
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Comment: C: package for pathway analysis
... I also like the package 'pcot2' written by Sarah Song. It checks all KEGG pathways by default but you can, with a little elbow grease, define your own genesets to test as well. I like it better the GSEA etc because it is a true multivariate test (Hotellings T-square) Martha Sent from my Verizon Wi ...
written 9.0 years ago by Martha Behnke100
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comparing Limma output from 2 different pre-processing methods
... Hello all, I am working with data with a very large number of differentially expressed genes (liver cancer samples), and wish to demonstrate for my advisor and committee the effect of choosing different pre-processing methods. To do this, I have normalized the data in several different ways and ge ...
cancer limma written 9.8 years ago by Martha Behnke100

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Popular Question 8.1 years ago, created a question with more than 1,000 views. For Having trouble with new brainarray CDF

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