User: sally_b86

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sally_b860
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Posts by sally_b86

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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 1 day 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 1 day 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 1 day 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 1 day ago by sally_b860 • updated 1 day ago by Michael Love15k
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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 5 days 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 7 days ago by sally_b860 • updated 7 days ago by James W. MacDonald45k
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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 8 days ago by sally_b860 • updated 8 days ago by Michael Love15k
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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 4 weeks ago by sally_b860
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Comment: C: Model matrix not full rank
... R1 samples represent the mice sacrificed in the same week. I was wondering if I can remove it from the analysis. Unfortunately, when I do PCA plot, it is clear that there's a variation among biological replicates (8 replicates per time point). I can consider that its a biological variation and not ...
written 4 weeks ago by sally_b860
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Comment: C: Model matrix not full rank
... sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 [4] LC_NUME ...
written 4 weeks ago by sally_b860

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