User: yk.gatc

gravatar for yk.gatc
yk.gatc0
Reputation:
0
Status:
New User
Location:
Last seen:
5 months ago
Joined:
8 months, 1 week ago
Email:
y******@gmail.com

Posts by yk.gatc

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answers
463
views
1
answers
Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... lfcShrink with "normal" and "apeglm" gives different volcano patterns (please see image attached). Is this expected behavior of different types of shrinkage methods? Or is it something odd here? https://imgur.com/a/N4Wwp ...
written 6 months ago by yk.gatc0
0
votes
1
answers
463
views
1
answers
Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... With the new code (developer version), lfcShrink estimation was done successfully with the following message  - > resLFC <- lfcShrink(dds, coef=22, type="apeglm", res=res) using 'apeglm' for LFC shrinkage Some rows did not converge in finding the MAP [1] DESeq2_1.19.36 apeglm_1 ...
written 7 months ago by yk.gatc0
0
votes
1
answers
463
views
1
answers
Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... I reinstalled the packages from Bioconductor, now I get different errors - > resLFC <- lfcShrink(dds, coef=22, res=res, type="apeglm") using 'apeglm' for LFC shrinkage Error in solve.default(o$hessian) : system is computationally singular: reciprocal condition number = 1.16041e-129 In addi ...
written 7 months ago by yk.gatc0
0
votes
1
answers
463
views
1
answers
Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... Thank you Michael for your time and support.  Btw, I am getting an error when I try to apply apeglm method -  res2 <- lfcShrink(dds, coef = 22, type = "apeglm", res = res) using 'apeglm' for LFC shrinkage Error in apeglm::apeglm(Y = Y, x = design, log.lik = log.lik, param = disps, : unus ...
written 7 months ago by yk.gatc0
0
votes
1
answers
463
views
1
answers
Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... Thanks for the suggestions. But with the design I am using, I cannot use coef argument with type="apeglm" to shrink LFC values. My objective here is to compare two treatment groups (with matched controls) which I supply as contrast=list(condA,condB). Do you have any suggestions to apply LFC shrinka ...
written 8 months ago by yk.gatc0
0
votes
1
answers
463
views
1
answers
Comment: A: DESeq2 LFC shrinkage is for designs with interactions
... Thanks Michael for the quick response.  I did try "ashr" method, but it gave me the following warning -  > resultsNames(dds) [1] "Intercept" "grp_Y_vs_X" "grpX.ind.n10" "grpY.ind.n10" "grpX.ind.n2" [6] "grpY.ind.n2" "grpX.ind.n3" "grpY.ind.n3" "grpX.ind.n4" "grpY.ind.n4" [11] "grpX. ...
written 8 months ago by yk.gatc0
1
vote
1
answer
463
views
1
answer
DESeq2 LFC shrinkage is for designs with interactions
... Hi, It seems like LFC shrinkage is not implemented for designs with interactions. Is there a way to get shrinked LFC values for designs with interactions? DESeq2_1.19.14 Thanks, YK ...
deseq2 lfcshrink written 8 months ago by yk.gatc0

Latest awards to yk.gatc

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: 293 users visited in the last hour