User: Wan Fahmi

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Wan Fahmi0
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Posts by Wan Fahmi

<prev • 5 results • page 1 of 1 • next >
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Same Values In Limma/Microarray Differential Expression
... Hello, I run limma for the differential expression of microarray microRNA data. I just wondering why am I getting the same value for the top list at least for 20 - 50 probeset. Is this a weird output from limma? The code as below: dat <- read.celfiles(list.celfiles("raw_data_dir")) es ...
microarray limma output differential expression written 6 months ago by Wan Fahmi0 • updated 6 months ago by RamRS22k
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Questionnaire for network-based visualization of RNA-seq data (NGS Graph Generator)
... Dear all My name is Fahmi and I am currently doing my PhD at The Roslin Institute about network-based visualization and usability of user interfaces in NGS Graph Generator (http://seq-graph.roslin.ed.ac.uk/). As a part of my work, I will be conducting a usability study on the NGS Graph Generator ...
software visualization rna-seq written 2.2 years ago by Wan Fahmi0
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Comment: C: Summary of alternative splicing from Cufflinks
... I also want to find a tool that can define alternative splicing from an RNA-seq output such as BAM file or transcript gtf file. There is also a tool can define alternative splicing such as AS_profile but least documentation on it, so it quite hard to use it.  ...
written 4.0 years ago by Wan Fahmi0
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Comment: C: Summary of alternative splicing from Cufflinks
... SpiceTrap may be useful and you also can run SpliceTrap using website here https://bioinformatics.cineca.it/rap/index.php ...
written 4.0 years ago by Wan Fahmi0
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Answer: A: Blast Db Version
... I do have a set of sequence reads (5k) and did a read-to-read comparison. I ran both formatdb and makeblastdb but it gave different answer. Why would it gave different answer?  Below is the different result between two different version of BLASTN (megablast) # BLASTN 2.2.29+ # Query: 5431875_t14_ ...
written 4.7 years ago by Wan Fahmi0

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