User: riccardo

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riccardo50
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Posts by riccardo

<prev • 93 results • page 1 of 10 • next >
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Bad replicate DESeq2
... Hello, Here: https://imgur.com/z7Fkyjv you can find the PCA of the experiment that I am analyzing. Cond1 e cond2 were designed to have an over expression of two different genes. The sample cond1 near to controls has an expression of that gene much less than the others biological replicates. In this ...
deseq2 written 4 months ago by riccardo50 • updated 4 months ago by Michael Love19k
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Comment: C: DESeq2 condition table
... I just realized that if I put "control" in the condition I get the message and checking the code I saw this: controlSynonyms <- c("control", "Control", "CONTROL") for (cSyn in controlSynonyms) { if (cSyn %in% lastDVLvls) { if (cSyn != lastDVLvls[1]) { message(past ...
written 4 months ago by riccardo50
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Comment: C: DESeq2 condition table
... Hello, I did again the same thing that I posted before but this time using the same approach but with different values in the condition table I got this message: it appears that the last variable in the design formula, 'condition', has a factor level, 'control', which is not the reference lev ...
written 4 months ago by riccardo50 • updated 4 months ago by Michael Love19k
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Comment: C: find fold change in DESeq2 results
... Thank you to all for the information. ...
written 16 months ago by riccardo50
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find fold change in DESeq2 results
... Hi, maybe I am doing something wrong but I cannot find a log2FoldChange inside the results of DESeq2: res = results(dds, contrast=c("cond", test, control)) dRes = as.data.frame(res) dRes$log2FoldChange[1] [1] 12.62795 dRes[dRes$log2FoldChange == 12.62795,] [1] baseMean log2FoldChange lfc ...
deseq2 written 16 months ago by riccardo50 • updated 16 months ago by Michael Love19k
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Comment: A: deseq2 course experiment
... Hi Michael, thank you for your help. My WT2 and WT5 are my controls at different times but what if later I will be only interested in the comparison of, for example, A2 vs B2 and A5 vs B5? Should I perform again the analysis excluding WT2 and WT5 from the table of counts used by DESeq2? Or is it be ...
written 16 months ago by riccardo50
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Comment: C: deseq2 course experiment
... Hi Michael, I think that I found the problem, removeBatchEffect wants the log counts so using the log2 of the counts normalized by DESeq2 it seems work, do you agree?   ...
written 16 months ago by riccardo50
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Comment: C: deseq2 course experiment
... Hi I think that there is a problem because some values are negative, what could be the problem?  I have also another question regarding this code: dat <- counts(dds, normalized = TRUE) idx <- rowMeans(dat) > 1 dat <- dat[idx, ] mod <- model.matrix(~cond, colData(dds)) mod0 < ...
written 16 months ago by riccardo50
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Comment: C: deseq2 course experiment
... Thank you! If I wanted the read counts normalized without batch effects could I use this command? removeBatchEffect(counts(dds, normalized = TRUE), covariates = as.matrix(ddssva@colData$SV1, ddssva@colData$SV2, ddssva@colData$SV3)) Thank you ...
written 16 months ago by riccardo50
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Comment: C: deseq2 course experiment
... Sorry I think that this is more correct: rldBlindTrueRemBatch = removeBatchEffect(rldBlindTrueCounts, covariates = as.matrix(ddssva@colData$SV1, ddssva@colData$SV2, ddssva@colData$SV3)) Since my ddsva@colData is:                cond          SV1         SV2         SV3            <factor> ...
written 16 months ago by riccardo50

Latest awards to riccardo

Popular Question 7 months ago, created a question with more than 1,000 views. For edgeR TMM values
Great Question 7 months ago, created a question with more than 5,000 views. For edgeR TMM values
Popular Question 16 months ago, created a question with more than 1,000 views. For edgeR TMM values
Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2 old versions
Great Question 16 months ago, created a question with more than 5,000 views. For DESeq2 FPKM normalization
Great Question 16 months ago, created a question with more than 5,000 views. For edgeR TMM values
Popular Question 18 months ago, created a question with more than 1,000 views. For DESeq2 and shrinkage of log2 fold changes
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 and ComBat
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 FPKM normalization
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 and ComBat

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