User: mforde84

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mforde84560
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Posts by mforde84

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Comment: C: Software for GO enrichment based on own DEGs and GO annotation.
... It sounds like OP wants to do a Fisher's or hyper geometric over-representation test for GO terms filtered by DEG. GSEA is different, though as you say it's preferable for a number of reasons. ...
written 11 days ago by mforde84560
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Comment: C: Software for GO enrichment based on own DEGs and GO annotation.
... Pathway analysis or gene set enrichment is not the same as Gene Ontology term enrichment / over-representation. You're measure two completely different things. Sure you can use GO terms and their gene constituents as pathways and ask interesting questions about whether those pathways are being cons ...
written 11 days ago by mforde84560
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Answer: A: Software for GO enrichment based on own DEGs and GO annotation.
... Try http://geneontology.org/page/go-enrichment-analysis A popular option in R is to use limma goana() function as well. ...
written 13 days ago by mforde84560
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Comment: C: Software for GO enrichment based on own DEGs and GO annotation.
... That's pathway enrichment which is different from gene ontology term enrichment. Loosly pathway analysis looks at centroid expression level of multiple genes within a given pathway then determines the probability that this is different from some group contrast. Whereas term enrichment, looks at the ...
written 13 days ago by mforde84560
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Answer: A: How fold change varies through out different microarray platforms?
... I think you're asking a question relating to meta-analysis against different array layouts. So for instance, how comparable is data from U133A vs U133B? That's a really good question and a hard one to answer. In order to do this, you need to subset your data from both platforms to include only probe ...
written 13 days ago by mforde84560
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Comment: C: Alignment time of TopHat (v.2.1.1) increases while increasing threads (using mul
... Try three threads :) ...
written 13 days ago by mforde84560
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Comment: C: Adding .txt or .fa extension to UnixExecutable
... the for loop is POSIX compliant. if by unixy you mean meaninglessly verbose with no added benefit to readability or speed, then i must respectfully disagree :) i mean why not: find ./ -maxdepth 1 -type f | xargs -n -P "$(grep -c ^processor /proc/cpuinfo)" -iFILES sh -c 'mv FILES FILES.txt' ins ...
written 15 days ago by mforde84560
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Comment: C: Alignment time of TopHat (v.2.1.1) increases while increasing threads (using mul
... If you have 4 cores, that means you can utilize the CPU to 400%. If you have 4 threads, that means you can run 4 processes simultaneously (roughly) each at 100% CPU load. If you run 8+ threads on a 4 core / 4 thread processor, that means that your still running 4 threads at 100% at a time, but that ...
written 15 days ago by mforde84560
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Comment: C: Alignment time of TopHat (v.2.1.1) increases while increasing threads (using mul
... Lol, you only have an finite number of threads, dude. http://ark.intel.com/products/80815/Intel-Core-i5-4590-Processor-6M-Cache-up-to-3_70-GHz ...
written 15 days ago by mforde84560
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Comment: C: Adding .txt or .fa extension to UnixExecutable
... Can you be a little clearer about what you want to do and why? A binary file is compiled byte code. It will always be interpreted as byte code regardless of what extension you put on it. Extensions really don't mean that much in linux, and that's especially the case for bash and sh. If what you wa ...
written 15 days ago by mforde84560

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