User: Matthew McCormack

Reputation:
180
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Trusted
Location:
United States
Last seen:
2 years, 3 months ago
Joined:
12 years, 7 months ago
Email:
m********@molbio.mgh.harvard.edu

Posts by Matthew McCormack

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
... In addition to GO terms, I find MapMan functional classifications very helpful. You can download them here: https://mapman.gabipd.org/mapman-download  You can also to UToronto's BAR website and add a list of AGI numbers and get functional classifications here: http://bar.utoronto.ca/ntools/cgi- ...
written 5 months ago by Matthew McCormack180
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Comment: C: DESeq2 ddsHTSeq error
... Thank you, Michael. This will give me a place to start checking. The first column is the gene names. I will check to see if they are equivalent in all files. Matthew On 5/25/2017 6:30 PM, Michael Love [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > < ...
written 2.3 years ago by Matthew McCormack180
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DESeq2 ddsHTSeq error
... I am running DESeq2 with 100 HTSeq files. My sampleTable is: sampleTable sampleName fileName condition 1 ate1-1_ah HTseq_ate1-1_ah_HTSeq.txt ate 2 ate1-2_ah HTseq_ate1-2_ah_HTSeq.txt ate 3 azf1-1_ah HTseq_azf1-1_ah_HTSeq.txt ...
deseq2 written 2.3 years ago by Matthew McCormack180 • updated 2.3 years ago by Michael Love25k
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Comment: C: P values from Deseq Analysis
... Can you apply DESeq to RPKM values ? I thought you had to use HTSeq, or something similar, to get integer counts for each gene for input into DESeq. Matthew On 5/10/2017 6:20 PM, spawar2 [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: suppor ...
written 2.4 years ago by Matthew McCormack180
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loading .bam file in CrispRVarients
... I am following the CrispRVarients User Guide and when I get to this command: reference=system(sprintf("B621_279062w_CF5_TAIR10_sort.bam %s:%s-%s", seqnames(gdl)[1], start(gdl)[1], end(gdl)[1]), intern = TRUE) I always get this error message: 'CreateProcess' failed to run 'D:\NGS_data\WEN_CR~1\ ...
crisprvariants written 2.7 years ago by Matthew McCormack180 • updated 2.7 years ago by helen.lindsay0
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Answer: A: Quality control on RNA-Seq (level 3) data from TCGA
... If you have the files in .fastq format you can use fastqc available from here: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Fastqc will work on zipped files, so you do not have to unzip them first. However, I think this format is what TGAC calls level 1 data. Level 3 data seems to me t ...
written 3.9 years ago by Matthew McCormack180
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Comment: C: P Value of 0?
... Thank for link, Ryan. I have started reading the paper and it is very helpful. ...
written 4.6 years ago by Matthew McCormack180
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Comment: C: P Value of 0?
...  Thanks, Ryan.  So, how is this different from just doing more manual log(2) cut off  in Excel or a Perl script ? ...
written 4.6 years ago by Matthew McCormack180
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Answer: A: P Value of 0?
... Hi Gordon,    So, to be clear, you would not recommend cutting off at, say FDR 0.05, and after that cutting off at log(2) of, say, >1 and < -1 ? Could you possibly elaborate in a few sentences the reasoning behind your above comment ? ...
written 4.6 years ago by Matthew McCormack180 • updated 4.6 years ago by Gordon Smyth38k
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best server maintenance practices
... I am not a Linux administrator, and I don't think the Linux administrators that we have understand our needs with regard to installing and keeping up to date programs that regularly update to newer versions. We have a few versions of R installed in various places on our server, as well a few version ...
linux R server written 5.0 years ago by Matthew McCormack180 • updated 5.0 years ago by James W. MacDonald51k

Latest awards to Matthew McCormack

Scholar 2.3 years ago, created an answer that has been accepted. For A: Quality control on RNA-Seq (level 3) data from TCGA
Scholar 3.9 years ago, created an answer that has been accepted. For A: Quality control on RNA-Seq (level 3) data from TCGA
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Quality control on RNA-Seq (level 3) data from TCGA

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