User: mmokrejs

gravatar for mmokrejs
mmokrejs0
Reputation:
0
Status:
New User
Location:
Last seen:
1 week, 4 days ago
Joined:
5 months, 3 weeks ago
Email:
m*******@fold.natur.cuni.cz

Posts by mmokrejs

<prev • 8 results • page 1 of 1 • next >
0
votes
0
answers
23
views
0
answers
ReportingTools: Error using packet 1 arguments must have same length
... Hi, I have some output from DESeq2 to be processed by ReportingTools. In thread https://support.bioconductor.org/p/115810/#115817 it turned out it is a ReportigTools issue. Would you please comment on this error, visible only in rendered figures? library(ReportingTools) desReport <- HTMLRe ...
reportingtools written 12 days ago by mmokrejs0
0
votes
1
answers
58
views
1
answers
Comment: C: DESeq2: Error using packet 1 arguments must have same length
... Thank you, Michael, I will open a new thread then. I added the ReportingTools tag but probably too late to notify its author. Would you please comment on these attempts, line by line? I am new to this and I do not really understand the underlying differences, hence the comments on lines commented o ...
written 12 days ago by mmokrejs0
0
votes
1
answers
58
views
1
answers
Comment: C: DESeq2: Error using packet 1 arguments must have same length
... > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /apps/gentoo/usr/lib64/librefblas.so.3.7.0 LAPACK: /apps/gentoo/usr/lib64/libreflapack.so.3.7.0 locale: [1] C attached base packages: [1] sta ...
written 12 days ago by mmokrejs0
0
votes
1
answer
58
views
1
answer
DESeq2: Analyzing just two normal+tumour pairs
... Hi,   I have RNAseq from two cancer+normal cases. I used salmon and proceeded with DESeq2. I do get the ./results/ directory out but the PDF figures are broken. The error message for example in boxplot.ENSG00000077454.15.pdf states: "Error using packet 1 arguments must have same length". The X-axis ...
deseq2 reporting tools written 12 days ago by mmokrejs0
0
votes
1
answers
393
views
1
answers
Comment: C: How to create tx2gene.gencode.v27.csv
... So here is what a friend helped me to stitch together:   wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gtf.gz wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gff3.gz wget ftp://ftp.ebi.ac.uk/pub/databa ...
written 19 days ago by mmokrejs0
0
votes
0
answers
89
views
0
answers
Comment: C: Rgraphviz installation fails in R with OpenBLAS
... I am having same issue here on Gentoo Linux with gcc-8.2.0. Although I do have system-wide grapviz-2.40.1-r1 installed through R-3.5.1 version 2.26.0 is being picked (while logs state 2.28.0). See https://gitlab.com/graphviz/graphviz/issues/1412 By switching to gcc-7.3.0 I can at least work around ...
written 19 days ago by mmokrejs0
0
votes
1
answers
393
views
1
answers
Comment: C: How to create tx2gene.gencode.v27.csv
... Hi Michael, thank you for your kind answer and I am sorry for the delay in my response, I thought I will receive an email if someone replies. Indeed, I have tximport-1.2.0 installed on the server: $ R R version 3.5.1 (2018-07-02) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statist ...
written 3 months ago by mmokrejs0
1
vote
1
answer
393
views
1
answer
How to create tx2gene.gencode.v27.csv
... Hi,    I am unable to follow up the tutorial at https://github.com/mikelove/tximport/blob/master/vignettes/tximport.Rmd I am getting: > library(readr) tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv")) Error: '/home/mmokrejs/R/x86_64-pc-linux-gnu-library/3.4/tximportData/ext ...
tximportdata written 5 months ago by mmokrejs0 • updated 5 months ago by Michael Love20k

Latest awards to mmokrejs

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 383 users visited in the last hour