User: Bioinformatics

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Posts by Bioinformatics

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how can I convert a sequence to number
... I am reading about a new package and I am interested in plotting logo of a protein sequence. The problem is that the author did not specify how one can convert the sequence to number https://www.bioconductor.org/packages/devel/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html#plot-an-amino- ...
motifstack written 29 days ago by Bioinformatics30 • updated 28 days ago by Ou, Jianhong1.1k
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Comment: C: how can I calculate FDR with no replicate
... @Aaron Lun Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 12 weeks ago by Bioinformatics30
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Comment: C: how can I calculate FDR with no replicate
... @Gordon Smyth Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 12 weeks ago by Bioinformatics30
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Comment: C: how can I calculate FDR with no replicate
... @ 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 12 weeks ago by Bioinformatics30
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Comment: C: how can I calculate FDR with no replicate
... @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 12 weeks ago by Bioinformatics30
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how can I calculate FDR with no replicate
... 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, ...
microarray edger written 12 weeks ago by Bioinformatics30 • updated 12 weeks ago by Gordon Smyth37k
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Comment: C: how to retrieve all attributes from biomart ?
... @James W. MacDonald gene ontology means you can find various information from any given gene. Look at http://www.geneontology.org    ...
written 4 months ago by Bioinformatics30
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Comment: C: how to retrieve all attributes from biomart ?
... @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 4 months ago by Bioinformatics30
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Comment: C: how to retrieve all attributes from biomart ?
... @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 4 months ago by Bioinformatics30
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how to retrieve all attributes from biomart ?
... 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', +                                     ...
biomart written 4 months ago by Bioinformatics30 • updated 4 months ago by James W. MacDonald49k

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