User: kmyers2

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kmyers220
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20
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New User
Location:
University of Wisconsin-Madison
Twitter:
@unionicola
Last seen:
2 months, 4 weeks ago
Joined:
9 months, 2 weeks ago
Email:
k******@wisc.edu

Posts by kmyers2

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Combining all columns in multiple files into one based on shared common field
... Thanks! When I try the join command you suggest though, it provides the following without running: usage: join [-a fileno | -v fileno ] [-e string] [-1 field] [-2 field] [-o list] [-t char] file1 file2 I'm not sure what to do. I've never used join before. I am able to join files ...
written 12 weeks ago by kmyers220
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Combining all columns in multiple files into one based on shared common field
... I have a set of 38 txt files that all have a similar format: the first column is gene ID and the remaining columns are expression data. I want to join all of these files into one and retain all columns if and only if the first column of gene IDs are the same. I have tried merge in Pandas, but get ...
python merge pandas join temp written 12 weeks ago by kmyers220
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Comment: C: Type checker error with bedtools intersect
... Thanks for the reply. This command was used to generate the file: bowtie genome.bowtie -M 1 -v 3 -q input.fastq --un input.-unaligned.fastq I guess I thought this would be a SAM file. ...
written 3 months ago by kmyers220
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Using GEOquery to download multiple expression data series files and then combine
... I need to combine all available expression data for a number of bacterial species. I have written a python script that can download all the relevant files from GEO for each species. However, when I look at the different series files, often the gene IDs are different. In order to combine all the data ...
ncbi geo expression array rna-seq R written 4 months ago by kmyers220 • updated 4 months ago by Kevin Blighe48k
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Low HTseq Feature Counts in Subset of RNA-seq Samples
... I am analyzing a set of 30 RNA-seq samples isolated from a non-model bacterial species. 24 of these samples are new experiments and 6 are re-analysis of a previously student's samples. All were isolated using the same growth conditions, isolation methods, etc. The 24 were sequenced at a different fa ...
htseq rnaseq feature counts alignment written 6 months ago by kmyers220
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Comment: C: Statistical Tests for Two Data Tables
... Thanks! I hadn't heard of Mentel's test. I've tried but need to read more to understand the results. I compared the matrix of all data and the matrix of the individual regulon and got a significants of 0.001 and a statistic r: 0.9113. I'll read more, but thanks for your help! ...
written 7 months ago by kmyers220
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Comment: C: Statistical Tests for Two Data Tables
... Thanks. You are interpreting my data correctly, yes. Is there a better way to compare two matrices? ...
written 7 months ago by kmyers220
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Statistical Tests for Two Data Tables
... I am curious if anyone has good ideas for this problem I have. I have a starting data set of ~4000 genes and 113 experimental conditions (data_frame of 'data'). I also have four predicted regulons made up of genes from the starting data set (26 genes ('a'), 16 genes ('b'), 16 genes ('c'), and 6 gen ...
R written 7 months ago by kmyers220
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Comment: C: EdgeR with Paired Sample Replicates
... Thank you very much! That makes sense to me and I really appreciate the help! ...
written 9 months ago by kmyers220
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Comment: C: EdgeR with Paired Sample Replicates
... Thanks! So if I understand, this will maintain the days in the comparison right? It is best to compare samples collected on the same day (ExpA vs CtrlA). I just want to make sure I'm understanding it correctly. ...
written 9 months ago by kmyers220

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