User: mictadlo

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mictadlo0
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Posts by mictadlo

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Comment: C: topGO - missing value where TRUE/FALSE needed
... The GOmapping.tsv looks like this: "V1" "V14" "sp0000005" "GO:0003723" "sp0000006" "GO:0016021" "sp0000007" "GO:0003700,GO:0006355,GO:0043565" "sp0000016" "GO:0046983" "sp0000017" "GO:0004672,GO:0005524,GO:0006468" How is possible to fix the problem with the quotes and spaces? Than ...
written 2 days ago by mictadlo0
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topGO - missing value where TRUE/FALSE needed
... Hi, I found here a tutorial how to use topGO. Unfortunately, I got missing value where TRUE/FALSE needed with the below code: > tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(1.5)) > topTags(tr) Coefficient: -1*Leaves.2 1*Leaves.3 logFC unshrunk.logFC logCPM PVal ...
topgo edger written 3 days ago by mictadlo0
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Comment: C: Saving output from glmTreat to a csv file?
... By any chance, do you know how it would be possible to create an R named vector where the names are genes and the values are p-values from `tr` without save `tr` to a file? ...
written 3 days ago by mictadlo0
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Saving output from glmTreat to a csv file?
... Hi, How is it possible save the output from glmTreat to a csv file? > tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(1.5)) > topTags(tr) Coefficient: -1Leaves.2 1Leaves.3 logFC unshrunk.logFC logCPM PValue FDR sp0090975 2.6 2.6 2.8 5.7e-14 2.7e-09 sp0037632 ...
edger rna-seq written 3 days ago by mictadlo0 • updated 3 days ago by Aaron Lun16k
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Comment: C: bias.data vector must have the same length as DEgenes vector!
... Hi, I took your suggested on board but I have a problem with nullp's DEgenes Argument (A named binary vector where 1 represents DE, 0 not DE and the names are gene IDs). In this paper they used the following to determine differential expression > tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2( ...
written 4 days ago by mictadlo0
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adding genes to edgeR
... Hi, I have the following read count table > rawCountTable <- read.table(paste0(basedir,"Htseq_read_counts/Sporobolus_pyramadalis_read_counts_mod_gene_names_modified.tsv"), header=TRUE, + row.names=1) > head(rawCountTable) X1916.MJO.0001_1 X1916.MJO.000 ...
edger written 7 days ago by mictadlo0 • updated 7 days ago by Aaron Lun16k
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bias.data vector must have the same length as DEgenes vector!
... Hi, I followed this paper until Pathway analysis because I wanted to replace it by goseq. > head(gene_len) V1 V2 V3 1 Length GC NA 2 sp0000001 6406 0.3535748 3 sp0000002 333 0.5495495 4 sp0000003 216 0.4583333 5 sp0000004 357 0.5602241 6 sp0000005 4808 0.3928869 ...
edger goseq written 7 days ago by mictadlo0 • updated 7 days ago by Aaron Lun16k
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gene length file for GOseq
... #!/usr/bin/env Rscript # based on https://www.biostars.org/p/84467/#84495 # source("https://bioconductor.org/biocLite.R") # biocLite("GenomicRanges") # biocLite("rtracklayer") biocLite("Rsamtools") library(GenomicRanges) library(rtracklayer) library(Rsamtools) GFFfile = "Sp.gff" FASTAfile = "Sp.faa ...
goseq written 9 days ago by mictadlo0
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Comment: C: Error in normSplitFactor(f, x)
... Thank you: `grl <- reduce(split(GFF, elementMetadata(GFF)$ID))` ...
written 9 days ago by mictadlo0
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Error in normSplitFactor(f, x)
... Hi, I found the below code here: > library(GenomicRanges) > library(rtracklayer) > library(Rsamtools) Loading required package: Biostrings Loading required package: XVector > > GFFfile = "snap_augustus.gff" > FASTAfile = "genome_29155.faa" > > #Load the annotation and redu ...
rtracklayer genomicranges goseq written 9 days ago by mictadlo0 • updated 9 days ago by Michael Lawrence9.5k

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