User: Adam Cornwell

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Adam Cornwell420
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Joined:
7 years, 9 months ago
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Posts by Adam Cornwell

<prev • 23 results • page 2 of 3 • next >
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Comment: C: Difference Between Oligo And Affy Packages For Affymetrix Gene St Array Pre-Proc
... I suppose I'll take the silence to mean "look at the code" or "post to the BioC list". ...
written 7.0 years ago by Adam Cornwell420
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Difference Between Oligo And Affy Packages For Affymetrix Gene St Array Pre-Processing
... Hello, I've got some Affymetrix Gene ST arrays I'm working with. My usual workflow is with Affy/Limma for Affymetrix 3' arrays, but I always see the Gene ST arrays brought up with Oligo and Aroma for pre-processing. Does the choice between Affy and Oligo actually make any difference in results, if I ...
normalization microarray affymetrix written 7.1 years ago by Adam Cornwell420 • updated 3.0 years ago by steve.s.sheridan0
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Comment: C: Cdf For Affymetrix Mouse Gene St 2.0?
... Thanks! I've seen that site before but it wasn't coming up in search results. That did the trick. ...
written 7.1 years ago by Adam Cornwell420
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Cdf For Affymetrix Mouse Gene St 2.0?
... We just got some new data back on Affy Mogene 2.0 ST arrays. I know this design has only been out for a couple of months, but does anyone know of any CDF files available that will work fine with Bioconductor? It looks like there's a chance of being able to get one of the files Affy provides in the ...
normalization microarray affymetrix written 7.1 years ago by Adam Cornwell420 • updated 7.1 years ago by UnivStudent380
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Comment: C: Wgcna Network Construction Issues & Best Practices?
... Since there haven't been any other answers- I asked someone who's had some correspondence with the authors of the package, and the suggested minimum number of samples is apparently 12. I have no other sort of backup or reasoning for this, but it sounds like a reasonable enough value. ...
written 7.6 years ago by Adam Cornwell420
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Wgcna Network Construction Issues & Best Practices?
... I have a microarray dataset which I was hoping to be able to process using a gene network construction algorithm, most notably WGCNA. I am having trouble determining if my current dataset is appropriate for network construction. I have tried a number of different subsets of probes, samples, and al ...
R network expression microarray written 7.6 years ago by Adam Cornwell420 • updated 7.6 years ago by Olga0
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Comment: C: Accounting For Vector Expression In Analyzing Microarray Data
... It looks like I was interpreting the experiment wrong... ...
written 7.6 years ago by Adam Cornwell420
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(Closed) Accounting For Vector Expression In Analyzing Microarray Data
... I'm using limma in Bioconductor for differential expression analysis of an Affymetrix data set. The goal is to determine the genes that are differentially regulated with the overexpression of an insert gene via a viral vector. The design is such that we have four sets of arrays- vector only, no vect ...
bioconductor expression microarray limma written 7.6 years ago by Adam Cornwell420
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Cell Type Marker Databases?
... Hi, I've been looking to see if there is any kind of public database or resource for cell type-specific markers. These would include genes for proteins that can uniquely identify a cell population using techniques such as FACS. I've tried a variety of different search terms, but haven't managed to c ...
database written 7.7 years ago by Adam Cornwell420 • updated 15 months ago by of20
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Comment: C: Limma Lmfit/Ebayes And P-Values Of 0?
... Update2: write.fit defaults to rounding to 3 digits, which doesn't seem to match the behavior of similar methods like topTable. I somehow missed that there's an argument in write.fit to specify the number to round to. Closing since it turns out this wasn't a great question. ...
written 7.8 years ago by Adam Cornwell420

Latest awards to Adam Cornwell

Popular Question 5.3 years ago, created a question with more than 1,000 views. For Automated Quality Analysis Pipeline For Affymetrix Gene St Arrays?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Methods For Comparing Microarrays From Different Datasets
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Limma Lmfit/Ebayes And P-Values Of 0?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Cdf For Affymetrix Mouse Gene St 2.0?
Student 5.3 years ago, asked a question with at least 3 up-votes. For Methods For Comparing Microarrays From Different Datasets
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Integrating A Local Galaxy Instance With Cluster Or Cloud Compute Resources?
Appreciated 6.3 years ago, created a post with more than 5 votes. For Wgcna Network Construction Issues & Best Practices?
Appreciated 6.3 years ago, created a post with more than 5 votes. For Integrating A Local Galaxy Instance With Cluster Or Cloud Compute Resources?
Good Question 6.3 years ago, asked a question that was upvoted at least 5 times. For Wgcna Network Construction Issues & Best Practices?
Good Question 6.3 years ago, asked a question that was upvoted at least 5 times. For Integrating A Local Galaxy Instance With Cluster Or Cloud Compute Resources?
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Wgcna Network Construction Issues & Best Practices?
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Cdf For Affymetrix Mouse Gene St 2.0?
Student 6.3 years ago, asked a question with at least 3 up-votes. For Wgcna Network Construction Issues & Best Practices?
Student 6.3 years ago, asked a question with at least 3 up-votes. For Integrating A Local Galaxy Instance With Cluster Or Cloud Compute Resources?
Student 6.3 years ago, asked a question with at least 3 up-votes. For Cell Type Marker Databases?

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