User: Moose123

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Moose1230
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Posts by Moose123

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Comment: C: Strange dispersion plot
... No problem, thanks a lot for your time and help.  ...
written 21 months ago by Moose1230
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Comment: C: Strange dispersion plot
... That worked! It is a bit as expected, the parents (of which we have four reps) at each side, and all offspring lines are in between (that have only 1 rep each). But very low PCs.   ...
written 21 months ago by Moose1230
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Comment: C: Strange dispersion plot
... It gives the following: > ntd <- normTransform(dds) > plotPCA(ntd) Error in .local(object, ...) :    the argument 'intgroup' should specify columns of colData(dds)   ...
written 21 months ago by Moose1230
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Comment: C: Strange dispersion plot
... Yes around 50,000 expressed genes ( I filtered out genes that have less than 10 counts in 90% of the samples), we are working with wheat. It is typical RNA-seq data at gene level. I made frequency plots of vst and rlog data, and the data does seem to be distributed normal, although shrinked a lot po ...
written 21 months ago by Moose1230
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Removal of outliers after library size correction, can I save this to my dds object?
... Hi, I looked for an answer but could not find it.. My supervisor replaced values of outliers in our expression data set to "NA", using the count data that is corrected for library size (means median-of-ratios). As we want to use the same processing steps, we want to assign these outliers also in my ...
deseq2 outliers written 21 months ago by Moose1230 • updated 21 months ago by Michael Love26k
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Comment: C: Strange dispersion plot
... Thank you for your comment. As design I consider every individual ("Line") a different condition, this because they all carry a different combination of the parental genomes, and each parent is considered one condition. We don't have 'real' different conditions like environmental stress.  The code ...
written 21 months ago by Moose1230
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Answer: A: Strange dispersion plot
... *edit: My excuses, this message can be deleted. I did not reply directly on your question.  ...
written 21 months ago by Moose1230
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Strange dispersion plot
... Hi, To explain our data, we are doing an exploratory network analysis, I have a dataset with 154 individuals (RIL population) which all have only one replicate. Also two parents, with 4 replicates each. We are working with around 50.000 genes. For the network analysis I use DESeq2 transformation wi ...
deseq2 dispersion written 21 months ago by Moose1230

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