User: sally_b86

gravatar for sally_b86
sally_b860
Reputation:
0
Status:
New User
Last seen:
1 year, 1 month ago
Joined:
2 years, 2 months ago
Email:
s********@hotmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by sally_b86

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
264
views
1
answer
Deseq2 within samples variability
... Hello,  Is there a way to correct for within sample variability?? PCA plot show that some replicates within some samples have higher variability than others? Does this affect alot the DEG output? And is it possible to avoid this other than removing highly variable samples? Thank you   ...
deseq2 within variability samples written 18 months ago by sally_b860 • updated 17 months ago by Michael Love26k
0
votes
0
answers
192
views
0
answers
ImpulseDE error message
... Hello,  I'm for the first time trying the ImpulseDE function, but unfortunately Im having some error messages like:  [1] "START: Prepare annotation table for internal usage" [1] "-------------------------------------------------------------------" [1] "Case condition: IR" [1] "DONE" [1] "######### ...
impulsede argument not a matrix. written 19 months ago by sally_b860
0
votes
1
answer
425
views
1
answers
Comment: C: Model matrix not full rank for condition-time experiment
... No direct relation between the samples but what Im saying that these mice are sacrificed in the same week. I have 8 series of mice each one constitute of certain time points sacrificed in the same week. So no relation between the samples. Im just explaining the naming 1, 2...  ...
written 2.1 years ago by sally_b860
0
votes
1
answer
425
views
1
answers
Comment: C: Model matrix not full rank for condition-time experiment
... Yes exactly this is what I want to compare and therefore the control is useless here, I used it in LRT of all conditions to have the same starting point. And this is the problem if I remove the control I won't be taking into consideration the changes from 0 to 45 min. Samples 1 in all conditions ar ...
written 2.1 years ago by sally_b860
0
votes
1
answer
425
views
1
answers
Comment: C: Model matrix not full rank for condition-time experiment
... Okey, I have in this case 3 conditions, control (no surgery), sham (surgery at 2 times, 45 min and 24 hrs) and non ischemic samples (mice with surgery and Ischemia reperfusion). I want to find out the genes varying by condition over time.  I have already done LRT test on each condition alone on the ...
written 2.1 years ago by sally_b860
0
votes
1
answer
425
views
1
answer
Model matrix not full rank for condition-time experiment
... Dear Michael,  Having this data, I want to study the effect of sham over time (each time point 8 replicates), unfortunately its giving error: Model matrix not full rank. Any solutions? Sample time condition Ctl.1 t0 control Ctl.2 t0 control Ctl ...
deseq2 model matrix not full rank written 2.1 years ago by sally_b860 • updated 2.1 years ago by Michael Love26k
0
votes
1
answer
441
views
1
answers
Comment: C: Anova test on gene expression data
... Actually I already did the first statistical filtering based on DESeq2 function, I want to do further analysis on the filtered genes but by Anova test on data normalized by DESeq2 on different conditions.  ...
written 2.1 years ago by sally_b860
0
votes
1
answer
441
views
1
answer
Anova test on gene expression data
... Hi,  Anyone knows a way to conduct anova test on gene expression data other than the DESeq2 and Limma package? Thank you  ...
anova gene expression written 2.1 years ago by sally_b860 • updated 2.1 years ago by James W. MacDonald52k
0
votes
1
answer
390
views
1
answer
PCA on deseq2 gene data set
... Hello,  Just a quick question please I plotted PCA plot of gene expression data in DESeq2 via the genespca function in pcaexplorer package, I got 2 subsets distributed in the second dimension, once checking the genes I found the 2 subsets represent up and down regulated genes. My question is what d ...
deseq2 pcaexplorer genespca written 2.1 years ago by sally_b860 • updated 2.1 years ago by Michael Love26k
0
votes
1
answer
441
views
1
answers
Comment: C: Model matrix not full rank
... batches correspond to library preparation, the samples that are prepared together for mRNA enrichment. ...
written 2.2 years ago by sally_b860

Latest awards to sally_b86

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: 174 users visited in the last hour