Question

Missing sample in recount3 data

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alex.dietrich • 0

@c7c12b17

Last seen 2.5 years ago

Germany

Hello,

I downloaded a dataset using recount3, which is supposed to have samples of two tissues from 15 patients (=30 samples). I only receive 29 samples though when I create the rse. The data published to GEO has all 30 samples available. I am guessing this one sample went missing due to some quality control settings? Where can I find these settings and is it possible to still get access to all 30 samples with recount3?

Best, Alex

recount3 • 1.2k views

ADD COMMENT • link 2.8 years ago • updated 2.7 years ago alex.dietrich • 0

score 0 · Answer 1 · 2022-03-30

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Leonardo Collado Torres ★ 1.1k

@lcolladotor

Last seen 16 days ago

United States

Hi Alex,

We would need a reprex or some code to be able help you more specifically. Though it could have been that that missing sample was not available when we ran Monorail for that study: either there was a connection problem or it was added at a later day.

See https://reprex.tidyverse.org/ or for more information about reprex.

Best, Leo

ADD COMMENT • link 2.8 years ago Leonardo Collado Torres ★ 1.1k

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Hi Leo,

Sorry you're right, here is the example code:

recount3_projects <- recount3::available_projects()
RP143467_project <- recount3_projects %>% filter(project == 'SRP143467')
SRP143467_rse <- recount3::create_rse(SRP143467_project)
dim(SRP143467_rse)
[1] 63856    29
f <- tempfile()
download.file(url = 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113764/suppl/GSE113764%5FhumanBATWAT%2Etxt%2Egz', destfile = f)
gse113764_file <- gzfile(f,'rt')
gse113764_counts <- read.csv(gse113764_file, sep = '\t', check.names = F)
gse113764_counts[,c('Accn','Symbol','GeneId')] <- NULL
dim(gse113764_counts)
[1] 218315     30

As you can see, the counts file from GEO has one more sample.

ADD REPLY • link 2.7 years ago alex.dietrich • 0