User: Ann Hess

gravatar for Ann Hess
Ann Hess340
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9 years, 6 months ago
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16 years, 7 months ago
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h***@stat.colostate.edu

Posts by Ann Hess

<prev • 34 results • page 1 of 4 • next >
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edgeR: common vs tagwise dispersion
... I am using edgeR to look for differentially abundant ?segments? between two groups (data generated using high throughput sequencing). I have 3 (pooled) biological reps per group and a total of 18760 segments (83 rows with zero count are removed by edger). As a first approach, I used the common dis ...
edger written 9.6 years ago by Ann Hess340 • updated 9.6 years ago by Mark Robinson1.1k
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edgeR: pseudocounts, logConc and logFC
... I am experimenting with edgeR for high throughput (next gen) sequence data and proteomics spectral count data and have a few questions. 1. Is it correct to think of the pseudocounts (pseudo.alt produced by estimateCommonDisp) as normalized counts? According to the edgeR vignette ?The pseudocounts ...
proteomics graph edger written 9.6 years ago by Ann Hess340 • updated 9.6 years ago by Mark Robinson1.1k
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DNAString: Error for long sequences
... I am having trouble creating long (~1000+ characters) DNAStrings. Specifically, I seem to get an error when R has to go to a new line in the command window when copy/pasting the sequence from an R script (with no breaks). I recently upgraded R and BioConductor, but previously I did not have this pr ...
go written 11.2 years ago by Ann Hess340 • updated 11.2 years ago by Martin Morgan ♦♦ 24k
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preprocessing for tiling arrays (preprocessCore package)
... I would like to perform RMA style preprocessing for tiling arrays. Based on previous discussion (thanks Ben and Jim!), it seems that the functions rma.background.correct() and normalize.quantiles() from the preprocessCore package are the easiest way to accomplish this. First of all, I am having tro ...
preprocessing written 11.3 years ago by Ann Hess340 • updated 11.3 years ago by Ben Bolstad1.2k
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rma for tiling arrays (oligo package)
... After creating an appropriate library using the makePDpackage, I am using the oligo package to open and work with Affymetrix Arabidopsis Tiling 1.0R Arrays. I am interested in using the rma function to background correct and normalize the data, but I am not sure how to map the processed data back t ...
oligo written 11.3 years ago by Ann Hess340 • updated 11.3 years ago by James W. MacDonald51k
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Warnings after makePDpackage
... I am trying to use makePDpackage for the Affymetrix Arabidopsis Tiling array. I ran the following code with no errors: library(makePlatformDesign) makePDpackage("At35b_MR_v04-2_TIGRv5.bpmap",file1="At35b_MR_v04.cif",m anufacturer="affymetrix",type="tiling") The (after exiting R), I ran the follow ...
written 11.3 years ago by Ann Hess340 • updated 11.3 years ago by James W. MacDonald51k
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CyberT versus Moderated t Comparison
... Does anyone happen to know of any papers which compare CyberT (Baldi and Long) to Moderated t (Smyth)? Ann ...
written 13.1 years ago by Ann Hess340 • updated 13.1 years ago by Darlene Goldstein230
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Affymetrix Poly-A Controls
... I have some questions about Affymetrix Poly-A Controls. The Affymetrix Data Analysis Fundamentals manual states that "Poly-A RNA controls can be used to monitor the entire target labeling process....All of the Poly-A controls should be called "Present" with increasing Signal values in the order of ...
probe written 13.1 years ago by Ann Hess340 • updated 13.1 years ago by James W. MacDonald51k
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RMA with few arrays
... I am wondering if it is appropriate to compute expression indices with RMA for only a small number of arrays (2 or 3). I have seen in previous posts that the expression indices can be identical for some probe sets across different arrays when using RMA with few arrays (because of the median polish ...
probe limma written 13.1 years ago by Ann Hess340 • updated 13.1 years ago by James W. MacDonald51k
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GO annotation/analysis for ath1121501
... I am working with data from ath1121501 (arabidopsis) arrays and I would like to do the following: 1. Subset a list of genes based on GO terms. For example, how many (and which) a given list belong to MF=metabolism. 2. Create a pie chart of the distribution of GO terms for my list. 3. Find stati ...
annotation go ath1121501 gotools gostats biomart written 13.2 years ago by Ann Hess340 • updated 13.2 years ago by Nianhua Li870

Latest awards to Ann Hess

Popular Question 9.6 years ago, created a question with more than 1,000 views. For edgeR: pseudocounts, logConc and logFC
Popular Question 9.6 years ago, created a question with more than 1,000 views. For Importing CDF file for custom array using makecdfenv
Popular Question 9.6 years ago, created a question with more than 1,000 views. For Li Wong PM-only "background" correction
Popular Question 9.6 years ago, created a question with more than 1,000 views. For heatmap-suppress col reordering/dendrogram?

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