User: kgorczak

gravatar for kgorczak
kgorczak10
Reputation:
10
Status:
New User
Location:
Belgium
Last seen:
9 months ago
Joined:
3 years, 3 months ago
Email:
k*******@up.poznan.pl

Posts by kgorczak

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answers
222
views
1
answers
Comment: C: How to find multiple overlaps with pairwiseAlignment()?
... Hi Hervé, Thank you for the very clear answer. Do I understand correctly that your script will only find two overlapping regions? Kind regards, K.   ...
written 9 months ago by kgorczak10
0
votes
1
answer
222
views
1
answer
How to find multiple overlaps with pairwiseAlignment()?
... I have two DNA sequences with two overlaps (one 557 bp long and one 140 bp long). Both overlaps are exactly the same between the DNA sequences (no mismatches between them). I would like to use the pairwiseAlignment() function in order to find them. However, that function returns always only one over ...
biostrings pairwisealignment written 9 months ago by kgorczak10 • updated 9 months ago by Hervé Pagès ♦♦ 13k
0
votes
0
answers
253
views
0
answers
limma model including duplicated probes
... I have a microarray data with many duplicated probe names (some are duplicated 2 times, some 10 times, some 35 times). The package limma offers a function avereps() to average expression across the same probe names, e.g. y.ave <- avereps(y, ID=y$genes$ProbeName). However, I do not want to run lmF ...
limma written 14 months ago by kgorczak10
0
votes
0
answers
1.5k
views
0
answers
Comment: C: Problem with summarizeOverlaps function
... Thank you a lot! if it's necessary, here is my e-mail: kgorczak@up.poznan.pl  ...
written 3.2 years ago by kgorczak10
0
votes
0
answers
1.5k
views
0
answers
Comment: C: Problem with summarizeOverlaps function
... I sent to you a link to dropbox (by accident maybe even twice). And here is the code I use: library("Rsamtools") bamfiles <- BamFileList("accepted_hits.bam") seqinfo(bamfiles) library("GenomicFeatures") txdb <- makeTxDbFromGFF("exon_havana.gtf", format="gtf", circ_seqs=character()) columns ...
written 3.2 years ago by kgorczak10
0
votes
0
answers
1.5k
views
0
answers
Comment: C: Problem with summarizeOverlaps function
... I even checked your profile ;-) but unfortunately I can see there only star signs instead of your email. Anyway, thank you and you will get my invitation to dropbox soon  ...
written 3.2 years ago by kgorczak10
0
votes
0
answers
1.5k
views
0
answers
Comment: C: Problem with summarizeOverlaps function
... Is it possible to get your e-mail? I will send you a link to my data on dropbox. Thank you. ...
written 3.2 years ago by kgorczak10
0
votes
0
answers
1.5k
views
0
answers
Comment: C: Problem with summarizeOverlaps function
... I followed your ideas: 1. I didn’t load the BiocParallel package. I got the same error: error 'validObject(.Object)': invalid class “SummarizedExperiment” object: 'rowRanges' length differs from 'assays' nrow 2. I selected chromosomes on the GRangesList object: library("Rsamtools") bamfile < ...
written 3.2 years ago by kgorczak10
1
vote
0
answers
1.5k
views
0
answers
Problem with summarizeOverlaps function
... I am following RNA-seq workflow (http://www.bioconductor.org/help/workflows/rnaseqGene/) using my data and I am trying to get read counts using summarizeOverlaps function. Unfortunately, it is impossible because of this error:  error 'validObject(.Object)': invalid class “SummarizedExperiment” obje ...
genomicalignments read counting written 3.2 years ago by kgorczak10
0
votes
1
answers
795
views
1
answers
Comment: C: problem using makeTxDbFromGFF and exonsBy() functions
... I installed a new version of R and reinstalled 'GenomicFeatures' and now everything works fine. Thank you. ...
written 3.3 years ago by kgorczak10

Latest awards to kgorczak

Popular Question 3.0 years ago, created a question with more than 1,000 views. For Problem with summarizeOverlaps function

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 371 users visited in the last hour