User: mico

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mico0
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Posts by mico

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Cannot find header.json in salmon index directory
... ``` > makeLinkedTxome function (indexDir, source, organism, release, genome, fasta, gtf, write = TRUE, jsonFile) { indexJson <- file.path(indexDir, "info.json") if (!file.exists(indexJson)) { indexJson <- file.path(indexDir, "header.json") } indexList <- fro ...
written 1 day ago by mico0
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Comment: C: Cannot find header.json in salmon index directory
... Hi Michael, I tried Salmon v1.0.0 with decoy-augmented transcriptomes today and when I imported using tximeta v1.5.6 the same error occurred... All files listed in the Salmon index directory: ``` complete_ref_lens.bin ctable.bin ctg_offsets.bin duplicate_clusters.tsv eqtable.bin info.json mphf.bin ...
written 1 day ago by mico0
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Comment: C: Cannot find header.json in salmon index directory
... Great, thanks so much Michael! ...
written 28 days ago by mico0
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Comment: C: Cannot find header.json in salmon index directory
... The latest one, v1.0.0 ...
written 28 days ago by mico0
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Cannot find header.json in salmon index directory
... I am running `tximeta` to import the salmon quantification data. When I link to the transcriptome using the following code: ``` indexDir <- file.path(dir, "transcriptome", "GRCh38.index") fastaPath <- c(file.path(dir, "transcriptome", "Homo_sapiens.GRCh38.cdna.all.fa.gz"), file ...
rna-seq salmon tximeta written 28 days ago by mico0
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Comment: A: How to access gene IDs associated with GO terms in GOSeq
... I found that if using org.Hs.egENSEMBL will return the GRCh38 ESIDs, while my former analyses used hg19 annotations.  > org.Hs.eg.db OrgDb object: | DBSCHEMAVERSION: 2.1 | Db type: OrgDb | Supporting package: AnnotationDbi | DBSCHEMA: HUMAN_DB | ORGANISM: Homo sapiens | SPECIES: Human | EGSOURC ...
written 13 months ago by mico0
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How to access gene IDs associated with GO terms in GOSeq
... I did the GO terms enrichment analysis using GOSeq, after that I want to access the esIDs in the significantly enriched terms. I tried to extract esIDs using org.Hs.eg.db and GO.db, according to the vignette and this post. For example using this category GO:0009063. library(org.Hs.eg.db) library( ...
go goseq ensemblid written 13 months ago by mico0 • updated 13 months ago by James W. MacDonald52k
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Comment: C: Get the countsFromAbundance as limma input
... I just drew the logCPM density plot, then I saw some weird lines in both raw & filtered plots (I have highlighted them with blue boxes):  https://drive.google.com/open?id=1qIvW-fiO3MC1QA_0-5putL307Brx7N6h I filtered the data using the filterByExpr() function. Do these lines mean some samples ha ...
written 15 months ago by mico0
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Comment: C: Get the countsFromAbundance as limma input
... Hi Smyth, thanks for your suggestion. Actually I tried both limma-trend and limma-voom, they didn't cost too much time. I found that if using limma-trend, the p-values in toptable are much higher and logFC are much smaller than those in limma-voom's. The following is my code: # limma-voom: v0 < ...
written 15 months ago by mico0
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Get the countsFromAbundance as limma input
... I am analyzing the TCGA data and doing the differential expression analysis for about 6,000 samples and 20,000 coding genes. I was suggested to use DESeq2 for DE analysis, but the DESeq() takes an extremely long time with 6,000 samples, therefore I would like to use the limma-voom instead. In the t ...
limma deseq2 differential expression tximport written 15 months ago by mico0 • updated 15 months ago by Gordon Smyth39k

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