User: skamboj

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skamboj0
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Posts by skamboj

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Creating the correct design
... I've been having some trouble with getting my pipeline to execute what I want. Below is my ColData, and what I would like to look at is the following. First I would like to look at the main effect of treatment. I tried Design = Clone + Treatment and did a contrast of VPA vs Unt, but the results were ...
deseq2 written 13 days ago by skamboj0 • updated 12 days ago by Michael Love24k
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Comment: C: Deseq issues - pipeline all of a sudden stopped working
... If you scroll down in the imgur link you'll see the coldata layout. Correct all genes are in the geneid column Also, geneNames = row.names(SMS_RNAseq) geneNames[duplicated(geneNames)] character(0) any(duplicated(colnames(SMSRNAseq))) [1] FALSE any(duplicated(rownames(SMSRNAseq))) [1] FALSE ...
written 20 days ago by skamboj0
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Comment: C: Deseq issues - pipeline all of a sudden stopped working
... posted an image of the coldata as well if you scroll down Also, geneNames = row.names(SMS_RNAseq) > geneNames[duplicated(geneNames)] character(0) > any(duplicated(colnames(SMS_RNAseq))) [1] FALSE > any(duplicated(rownames(SMS_RNAseq))) [1] FALSE ...
written 21 days ago by skamboj0
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Comment: C: Deseq issues - pipeline all of a sudden stopped working
... gene_count_matrix <- as.matrix(read.csv("file.csv", row.names = "gene_id")) SMS_RNAseq <- read.csv("RNAseq.csv", row.names = "ids") https://imgur.com/a/hDG7Av6 Current error: Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning mess ...
written 21 days ago by skamboj0
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Comment: C: Deseq issues - pipeline all of a sudden stopped working
... any(duplicated(rownames(gene_count_matrix))) [1] FALSE > geneNames = row.names(gene_count_matrix) > geneNames[duplicated(geneNames)] character(0) https://imgur.com/a/hDG7Av6 Current error: Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warn ...
written 21 days ago by skamboj0
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Deseq issues - pipeline all of a sudden stopped working
... The following was working just fine last week, however, I keep getting different errors all of a sudden and I don't know why I've been getting either: duplicate 'row.names' are not allowed when I delete row.names I get: ncol doesn't equal ncount or I get that there are neg values in my count dat ...
deseq2 written 21 days ago by skamboj0 • updated 21 days ago by Michael Love24k

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