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User: Bioinformatics

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Posts by Bioinformatics

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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 24 days 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 24 days 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 24 days 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 24 days 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 24 days ago by Bioinformatics30 • updated 24 days ago by Gordon Smyth36k
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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 11 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by Bioinformatics30 • updated 11 weeks ago by James W. MacDonald49k
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Dseq2 gives the same results no matter the condition ???
... 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 ...
dseq2 written 7 months ago by Bioinformatics30

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