User: sally_b86

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sally_b860
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Posts by sally_b86

<prev • 17 results • page 1 of 2 • next >
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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 5 months ago by sally_b860 • updated 5 months ago by Michael Love20k
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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 7 months ago by sally_b860
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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 12 months ago by sally_b860
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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 12 months ago by sally_b860
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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 12 months ago by sally_b860
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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 12 months ago by sally_b860 • updated 12 months ago by Michael Love20k
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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 12 months ago by sally_b860
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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 12 months ago by sally_b860 • updated 12 months ago by James W. MacDonald48k
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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 13 months ago by sally_b860 • updated 13 months ago by Michael Love20k
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Comment: C: Model matrix not full rank
... batches correspond to library preparation, the samples that are prepared together for mRNA enrichment. ...
written 13 months ago by sally_b860

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