User: maleknias

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maleknias40
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Posts by maleknias

<prev • 6 results • page 1 of 1 • next >
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Answer: A: NA values of count matrix in class DESeqDataSet
... Dear all I used all your guide but unfortunately all of them have the last same error !! first: > assay(rse_gene)=assay(rse_gene)[apply(assay(rse_gene), 1, function(x) sum( is.na(x) ))==0,] > dds <- DESeqDataSet(rse_gene, design = ~ disease.status) second: >assay(rse_gene)=assay(r ...
written 14 days ago by maleknias40
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NA values of count matrix in class DESeqDataSet
... Dear all Hi I downloaded a data set in class "RangedSummarizedExperiment" from "https://jhubiostatistics.shinyapps.io/recount/". I want to find differential expression genes. My code is : > load("~/Downloads/rse_gene.Rdata") > class(rse_gene) **[1] "RangedSummarizedExperiment" attr(,"pa ...
recount rna-seq written 21 days ago by maleknias40
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Tutorial: One of the easy way to achieve read count and RPKM file
... 1- You can go to web: https://jhubiostatistics.shinyapps.io/recount/ 2- Type your study ID in search box, like; SRP066834. 3- Based on any biological requirement like gene, exon, junction or phenotype, you can download read count table, RSE (RData file) and link to other information. 4- If you wa ...
tutorial rna-seq written 9 weeks ago by maleknias40 • updated 9 weeks ago by WouterDeCoster22k
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Comment: C: calculate RPKM from read count and gff by galaxy
... thanks a lot. It seems cool. could you guide me "how I can make .count file" ?? Is this make by "Count.seqs" and "mothur_toolsuit" ? ...
written 9 weeks ago by maleknias40
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Comment: C: calculate RPKM from read count and gff by galaxy
... Thanks but it's not useful for me. I want to save time and because sample size is big i want use table of read-count. so do it again from the beginning is not cost effective!! ...
written 9 weeks ago by maleknias40
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calculate RPKM from read count and gff by galaxy
... Hi ! I have a table (58037×117) contain scaled read count for 117 sample (case and control) and gff and gtf file. Considering of RPKM calculation: RPKM=(row number of reads/exon length) ×(1000 000 / number of mapped reads in the sample) how can I get a table (58037×117) contain RPKM?? Is it solutio ...
rna-seq written 9 weeks ago by maleknias40 • updated 9 weeks ago by EagleEye4.7k

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