User: carandres74

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Posts by carandres74

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How to normalized SWATH proteomic data?
... Hello I´m trying to normalize proteomic SWATH data from a proteomic analysis of CSF. I´ve try the DESeq2 package without success. Could any one recommend a specific R package or way to do this? Kind regards, CA ...
proteomics swath written 21 months ago by carandres740 • updated 21 months ago by Laurent Gatto840
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Answer: A: DESEQ2 and continuous data
... Hello This is what i was trying to do in order to normalize the data df = as.matrix(x) df[df==0]=NA kdf = knnImputation(df) cds=estimateSizeFactorsForMatrix(kdf) ndf=kdf/rbind(rep(list(cds))) boxplot(log(ndf)) Witch actually gives a pretty normalized box plot, but when trying to plot svd using ...
written 21 months ago by carandres740
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Answer: A: DESEQ2 and continuous data
... Hello This is what i was trying to do in order to normalize the data df = as.matrix(x) df[df==0]=NA kdf = knnImputation(df) cds=estimateSizeFactorsForMatrix(kdf) ndf=kdf/rbind(rep(list(cds))) boxplot(log(ndf)) Witch actually gives a pretty normalized box plot, but when trying to plot svd using ...
written 21 months ago by carandres740
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Answer: A: DESEQ2 and continuous data
... Hello Micheal I have SWATH proteomic data from cerebrospinal fluid. This is continuous data. Hope this answers your questions Best, CA   ...
written 21 months ago by carandres740
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DESEQ2 and continuous data
... Hello My name is Carlos. I am PhD student working on proteomic analysis from CSF. I am currently using the DESeq2 package in R to analyze the data, and wanted to ask if it is ok to use the negative binomial distribution on continuos data? Is the correction factor in the DESeq2 package based on a ra ...
proteomics deseq2 written 21 months ago by carandres740

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