User: csoneson

gravatar for csoneson
csoneson70
Reputation:
70
Status:
Trusted
Location:
Switzerland
Last seen:
an hour ago
Joined:
3 years, 7 months ago
Email:
c***************@gmail.com

Posts by csoneson

<prev • 7 results • page 1 of 1 • next >
1
vote
0
answers
150
views
0
answers
Comment: C: Error in checkForRemoteErrors(val) : QuasR: can't pass alignment parameters
... As Hans-Rudolf already mentioned, changing the QuasR alignment parameters for bisulfite data is not recommended. Regarding the error, what other parameter combinations did you try to conclude that you "always get the following error [...] no matter what the parameters are"? I can reproduce this erro ...
written 5 days ago by csoneson70
2
votes
1
answer
168
views
1
answers
Comment: C: Kallisto output with DEXSeq
... You can do round(counts) to get a matrix of integers. Also note that if you previously did differential gene expression analysis with DESeq2, your count matrix is probably on the gene level. For DEXSeq, you need a transcript-level count matrix (i.e., by setting txOut=TRUE in the tximport call).  ...
written 3 months ago by csoneson70
2
votes
1
answer
168
views
1
answers
Comment: C: Kallisto output with DEXSeq
... One option is to import the kallisto output into R with tximport (set txOut=TRUE to get the transcript-level count matrix). Then you can use DEXSeqDataSet() to create the DEXSeqDataSet object. You'll need to provide the featureID (which would be the rownames of the count matrix) and the groupID (whi ...
written 3 months ago by csoneson70
0
votes
1
answer
655
views
1
answers
Comment: C: tximport returns NA counts
... True, but that was only for 50 cells, for which txOut=FALSE also worked, so I guess it is not yet clear whether there is a set of cells for which txOut=TRUE works but txOut=FALSE doesn't. ...
written 14 months ago by csoneson70
1
vote
1
answer
655
views
1
answers
Comment: C: tximport returns NA counts
... I wonder if this could have to do with the automatic determination of the column types by read_tsv. By default I think it uses the first 1,000 values to determine the column type, and if these values are all 0 it may try to read the whole column as integers. This caused problems for me once (albeit ...
written 14 months ago by csoneson70
0
votes
1
answer
331
views
1
answers
Comment: C: how to specify the number of cores used by IHW
... Hi Vlad, thanks for your reply. I tried both your suggestions (I set OMP_FLAG="--disable-openmp" on line 96 in the configure file, my line 62 is about gcc), reinstalled lpsymphony and IHW from source, started new sessions, but unfortunately IHW still uses all the available cores on the machine. I'l ...
written 15 months ago by csoneson70
2
votes
1
answer
331
views
1
answer
how to specify the number of cores used by IHW
... Hi, when I run IHW on our server it uses lots of computational resources (at least 20 cores). I can't seem to find any way to modify this in the call to ihw(). Is there a way to reduce the number of cores used by IHW? Thanks! Example code (from the IHW package) and session info: library(IHW) X ...
ihw lpsymphony written 15 months ago by csoneson70 • updated 15 months ago by vladislav.kim10

Latest awards to csoneson

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: 151 users visited in the last hour