User: ap3637

gravatar for ap3637
ap36370
Reputation:
0
Status:
New User
Location:
Last seen:
1 month ago
Joined:
2 months, 4 weeks ago
Email:
a*****@columbia.edu

Posts by ap3637

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answers
72
views
1
answers
Comment: C: DESeq failure after update: unable to find an inherited method for function mcol
... I seem to have resolved it, though I'm not sure exactly why. I updated devtools and roxygen packages and it seems to work again for some reason.   ...
written 4 weeks ago by ap36370
0
votes
1
answers
72
views
1
answers
Comment: C: DESeq failure after update: unable to find an inherited method for function mcol
... I get the following.  Shows 0 columns when i do this, but the dds shows 313.   This is really strange. > mcols(dds) DataFrame with 58233 rows and 0 columns ...
written 4 weeks ago by ap36370
0
votes
1
answer
72
views
1
answer
DESeq failure after update: unable to find an inherited method for function mcols for signature Rle
... I'm running DESeq2 and just updated all of my packages.  Now suddenly I can't run several DESeq functions, rlog, varianceStabilizingTransformation, and DESeq functions now all throw this error.     Here is my session info:   > sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-apple ...
deseq deseq2 R version compatibility written 4 weeks ago by ap36370 • updated 4 weeks ago by Michael Love14k
0
votes
1
answers
132
views
1
answers
Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Ok great, that's good to know.  So assuming the "estimating dispersions" goes through, for future reference for anyone who encounters this problem, try VST instead of rlog, and update your R packages.   My guess is that the rlog might have failed somehow in the larger data set, if I had to guess wh ...
written 6 weeks ago by ap36370
0
votes
1
answers
132
views
1
answers
Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Update: It seems like it's getting past this phase using VST and updated R packages.  At "estimating dispersions" now, so hopefully everything will go through. I did receive the following warning, but maybe it's okay.   27 rows did not converge in beta, labelled in mcols(object)$betaConv. Use lar ...
written 6 weeks ago by ap36370
0
votes
1
answers
132
views
1
answers
Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Thanks for your reply.  The output you requested is too many characters to post here directly, so here is a link to that information. https://justpaste.it/1c00t   Thanks very much for your help, the point about the releveling is also very useful.  I'm going to try to update some packages that are ...
written 6 weeks ago by ap36370
0
votes
1
answers
132
views
1
answers
Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... Yes, using version 1.16. ...
written 6 weeks ago by ap36370
0
votes
1
answer
132
views
1
answer
What causes this DESeq2 error at "fitting model and testing"?
... I am using DESeq2 on a pretty large dataset.  I have mock and infection conditions for several mouse lines at 3 time points.  My goal is to contrast each line at each timepoint with it's corresponding mock at the same timepoint.  Previously I split the data into smaller subsets by line, but now I'm ...
deseq2 error differential expression written 7 weeks ago by ap36370
0
votes
1
answers
352
views
1
answers
Comment: C: DESeq2 design matrix with a single mock and multiple timepoints
... Thanks for your reply Michael.  This is really helpful.  I actually had tried this before using the composite column, Virus_Time, in the data file I provided.  I had believed that it wasn't the right thing to do because the resultsNames(dds) seemed pretty random, but it turns out I had not re-levele ...
written 12 weeks ago by ap36370
1
vote
1
answer
352
views
1
answer
DESeq2 design matrix with a single mock and multiple timepoints
... So I have a problem with a dataset I'm working on. Here is information about the samples.   Three viruses at three timepoints: Virus1_day1, Virus1_day3, Virus1_day8. Virus2_day1, Virus2_day3, Virus2_day8. Virus3_day1, Virus3_day3, Virus3_day8. And mock samples at a single timepoint: Mock_day6   ...
deseq2 design matrix written 12 weeks ago by ap36370 • updated 12 weeks ago by Michael Love14k

Latest awards to ap3637

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: 281 users visited in the last hour