User: RossCampbell

gravatar for RossCampbell
RossCampbell140
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USA/Frederick
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15 hours ago
Joined:
9 years, 1 month ago
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r*************@gmail.com

Posts by RossCampbell

<prev • 22 results • page 1 of 3 • next >
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Hypergeometric test - Defining the gene universe
... When doing a hypergeometric test for pathway enrichment, is there a generalized accepted way of defining the total "gene universe". I am debating two possible numbers: 1) the number of probes on the microarray that was used to generate the data in the first place, and 2) the total number of genes fr ...
hypergeometric test gene set enrichment written 3.0 years ago by RossCampbell140 • updated 3.0 years ago by Renesh1.9k
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Answer: A: Merge txt files in R into single Excel
... If you put all 600 files (and nothing else) in their own directory, you can use `list.files()` to pull in all 600 file names into a variable, then read each one individually and append it to a new data frame with either `rbind()` or `cbind()`, depending on whether you want to append each new file as ...
written 3.4 years ago by RossCampbell140
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Comment: C: how to incorporate R script in perl program and then run it from perl
... If you truly need to run R within Perl, you may want to look up the `system` function in Perl. You could write your R script to do all the calculations it needs, and call it from your Perl script with `system('Script.R')`. However, a more "correct" and adaptable way would probably be to write two in ...
written 3.5 years ago by RossCampbell140
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Comment: C: The most popular Alternative to David?
... I like the [Gene Ontology Consortium][1] [1]: http://geneontology.org/ ...
written 3.6 years ago by RossCampbell140
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WGCNA: Output gene lists from consensus network modules
... I am using WGCNA to create a consensus network from two different gene expression data sets. I want to do some downstream analysis with the modules that came out of this, so I would like to output the genes comprising each module. I know how to do this when dealing with modules from individual netwo ...
wgcna written 3.8 years ago by RossCampbell140 • updated 2.6 years ago by baldauf30
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Comment: C: Heatmap In R-Wgcna-->Error While Plotting Tom
... The best method would be to keep all the data I believe. WGCNA is designed to be an unsupervised process, so selecting rows with threshold differences would potentially skew the clustering process. It would be better to keep all the data intact and run the full data set on a higher power computer. I ...
written 3.9 years ago by RossCampbell140
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Comment: C: Heatmap In R-Wgcna-->Error While Plotting Tom
... I just opened it in Excel and chopped off a bunch of columns and about half the rows. Obviously that messes up the data, I just did that to test the idea. I'm going to try running the complete data set on a high-performance cluster hopefully later today. ...
written 3.9 years ago by RossCampbell140
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Comment: C: Heatmap In R-Wgcna-->Error While Plotting Tom
... I had the same error, maybe what worked for me will work for you. I suspected it may be due to input size and memory issues, and reduced my input from 35 observations of ~8000 genes to 15 obs of about 2500 just to test it out. The smaller data set plotted perfectly just like in the tutorial. I have ...
written 4.0 years ago by RossCampbell140
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Comment: C: Why Is One Fasta File Indexed Differently From The Others Using Bioperl'S Db::Fa
... Update: This issue was resolved when I installed Ubuntu updates this morning. I don't know what fixed, but there was apparently something behind the scenes that wasn't working right, but it's fine now. ...
written 6.9 years ago by RossCampbell140
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Comment: C: Why Is One Fasta File Indexed Differently From The Others Using Bioperl'S Db::Fa
... They are all unique. grep returned: chr10.fa:>chr10 chr11.fa:>chr11 chr12.fa:>chr12...and down through the list. They all are unique and match their filename. ...
written 6.9 years ago by RossCampbell140

Latest awards to RossCampbell

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Split Data From A Csv Cell Into Smaller Cells
Popular Question 5.6 years ago, created a question with more than 1,000 views. For A Pwm With Gapped Alignments In Biopython
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Parsing A Fasta File By Columns
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Split Data From A Csv Cell Into Smaller Cells
Student 5.8 years ago, asked a question with at least 3 up-votes. For A Pwm With Gapped Alignments In Biopython
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Split Data From A Csv Cell Into Smaller Cells
Supporter 6.7 years ago, voted at least 25 times.
Autobiographer 6.7 years ago, has more than 80 characters in the information field of the user's profile.

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