The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

User: k.vitting.seerup

Reputation:
60
Status:
Trusted
Location:
European Union
Last seen:
5 days, 11 hours ago
Joined:
3 years, 8 months ago
Email:
k***************@gmail.com

Posts by k.vitting.seerup

<prev • 32 results • page 1 of 4 • next >
1
vote
1
answer
44
views
1
answers
Comment: C: Does IHW use the supplied alpha for the correction calculations?
... Than you for taking the time to provide such a detailed answer! ...
written 5 days ago by k.vitting.seerup60
6
votes
1
answer
44
views
1
answer
Does IHW use the supplied alpha for the correction calculations?
... When using IHW one have to provide an alpha value to the ihw function. Is this alpha used in some manner in the calculation of the weighted p-values? Basically if I at a later stage decide to use another alpha cutoff than I used to run IHW do i need to re-run IHW or can I just apply it directly to t ...
deseq2 ihw written 6 days ago by k.vitting.seerup60 • updated 5 days ago by Nikos Ignatiadis160
0
votes
1
answer
66
views
1
answers
Comment: C: Bug in rtracklayer::import of amino acid fasta sequences
... Is there in practice any difference between that and using Biostrings::readAAStringSet() ? Would you recomend using Biostrings::readDNAStringSet() or rtracklayer::import() for DNA fasta files? ...
written 22 days ago by k.vitting.seerup60
3
votes
1
answer
66
views
1
answer
Bug in rtracklayer::import of amino acid fasta sequences
... I just found a problem with rtracklayer's import function when importing amino acid fasta (also the default way of storing amino acid sequences. (E.g. the "Protein-coding transcript translation sequences" at [Gencode genes official site][1])). Here is an easy to reproduce example: ### Define l ...
biostrings rtracklayer fasta import written 23 days ago by k.vitting.seerup60 • updated 23 days ago by Michael Lawrence10k
0
votes
1
answer
84
views
1
answers
Comment: C: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
... Unfortunatly not - you need transcript expression. That can be done with the tools discussed in the vignette here. ...
written 10 weeks ago by k.vitting.seerup60
0
votes
1
answer
84
views
1
answers
Answer: A: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
... Nope. But what you can do is use IsoformSwitchAnalyzeR to run DEXSeq - acutally DEXSeq is the default statistical engine (via the isoformSwitchTestDEXSeq() function) so you can just start from the top of the vignette. Please note that if you have >2 conditions IsoformSwitchAnalyzeR will do all p ...
written 10 weeks ago by k.vitting.seerup60
1
vote
1
answer
716
views
1
answers
Comment: C: Tximport with RSEM error
... You need to create a vector which contains the path to all the files you want to import. So if you have 3 files you want to import the vector need to contain the path to all of them. Right now you just have a string pointing to the parent directory. ...
written 3 months ago by k.vitting.seerup60
0
votes
0
answers
100
views
0
answers
Comment: C: What assays are distributed with Recount TX data
... Thanks! You should have added that as an answer so I could mak it as solved :-) ...
written 3 months ago by k.vitting.seerup60
1
vote
0
answers
100
views
0
answers
What assays are distributed with Recount TX data
... When downloading Recount2 tx-dataset (either via the R package or via their website) such as this dataset I get a RangedSummarizedExperiment which contain 4 assays: assays(rse_tx) "fragments" "ses" "scores" "df" Fragments are self-explanatory (counts from paired end data) - but what are the ...
0
votes
0
answers
105
views
0
answers
Comment: C: error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnal
... Why does cryptic error messages not belong here? ...
written 4 months ago by k.vitting.seerup60

Latest awards to k.vitting.seerup

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 16.09
Traffic: 388 users visited in the last hour