## User: Bioinformatics

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#### Posts by Bioinformatics

<prev • 64 results • page 1 of 7 • next >
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... @Aaron Lun Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 24 days ago by Bioinformatics30
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... @Gordon Smyth Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 24 days ago by Bioinformatics30
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... @ Aaron Lun I did read that part for sure, I cannot estimate the dispersion because I don't have many housekeeping genes so I set it as 0.4 which I think it is a good number between 0.1 and 0.6. Yes  estimateGLMCommonDisp does not work due to problem you mentioned. I am just wondering if there i ...
written 24 days ago by Bioinformatics30
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... @Gordon Smyth these are normalized expression not count. so it means if people do not use raw count, it won't be trusted? I have read many papers they published in science with FMPK which is normalized count by length of gene analyzed by edger !! (I personally do not like FMPK but just as example. ...
written 24 days ago by Bioinformatics30
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... Hi, I have a representative data like this. the first column is control and second is treated df<- structure(list(col1A = c(1.64, 0.03, 0, 4.202, 2.981, 0.055, 0, 0.002, 0.005, 0, 0.002, 0.649, 2.55, 2.762, 6.402, 0.91, 0.037, 0, 5.757, 3.916, 0.022, 0, 0, 0.003, 0, 0.262, 0.136, ...
written 24 days ago by Bioinformatics30 • updated 24 days ago by Gordon Smyth36k
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... @James W. MacDonald gene ontology means you can find various information from any given gene. Look at http://www.geneontology.org    ...
written 11 weeks ago by Bioinformatics30
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... @James W. MacDonald basically I am trying to do gene onthology. there are 100 packages but I prefer to retrieve data from UniProt or ensemble.  ...
written 11 weeks ago by Bioinformatics30
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... @James W. MacDonald   I just made the parsing smaller in order to show I have tried a lot but I cannot figure out what the problem is. For example  hsapiens_inf <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id', +                                    'ensembl_peptide_id','ensembl_e ...
written 11 weeks ago by Bioinformatics30
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... Basically I want to extract all attributes for several genes ,  when I use the following as example, I get an error , would anyone know why? hsapiens_inf <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id','ensembl_peptide_id','ensembl_exon_id', +                                     ...
written 11 weeks ago by Bioinformatics30 • updated 11 weeks ago by James W. MacDonald49k
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... Hello,  I am trying to understand why Dseq2 gives me the same result if I set my condition differently ? I use Raw count values  First way to do  condition <- factor(c(rep("Normal", 10),rep("Tumor", 11)))​​ dds <- DESeqDataSetFromMatrix(dfm, DataFrame(condition), ~ condition)​ keep <- r ...
written 7 months ago by Bioinformatics30

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Popular Question 20 months ago, created a question with more than 1,000 views. For unable to update packages: foreign, Matrix

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