User: catglen012

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catglen0120
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Posts by catglen012

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Answer: A: Issue with DESeq: when using DESeqDataSet object what to put under argument desi
... Would this be a solution to this: dds$group <- factor(paste0(dds$celltype, dds$condition)) design(dds) <- ~ group dds <- DESeq(dds) resultsNames(dds) # e.g. for condition KO cell type 2 vs cell type 1 results(dds, contrast=c("group","2KO","1KO")) # e.g. for cel ...
written 3 months ago by catglen0120
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Issue with DESeq: when using DESeqDataSet object what to put under argument design when there are 3 variables
... Hello! My ultimate goal is for each locality, see how males and females are differentially expressed during each separate life stage. Example: In Chicago (locality), how is my plant at the protonema stage, differentially expressed in males compared to females? When I construct my object dds, I w ...
R deseq2 rna-seq written 3 months ago by catglen0120
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Comment: C: Issue with DESeq: unable to find an inherited method for function (exprs) for si
... I was not sure of what it meant since I am following a tutorial/ beginner, but thank you so much! This solved my problem! ...
written 3 months ago by catglen0120
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Issue with DESeq: unable to find an inherited method for function (exprs) for signature DESeqTransform
... Hello! I am trying to create a heatmap but I am unable to do so because it seems like an object "exprs" is masked: > heatmap.2(exprs(vsdFull)[select,], col = hmcol, trace="none", margin=c(10, 6)) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ...
R deseq rna-seq written 3 months ago by catglen0120 • updated 3 months ago by WouterDeCoster35k
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Comment: C: Issue with DESeq2: Unable to create colData because "Error in data[[rowvar]]"
... Thank you Kevin! I tried changing my file from a .csv file to a .txt file and that worked! I was able to upload my data and obtain: > all(rownames(colData) %in% colnames(countData)) [1] TRUE > countData <- countData[, rownames(colData)] > all(rownames(colData) == colnames(countData)) [ ...
written 3 months ago by catglen0120
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Issue with DESeq2: Unable to create colData because "Error in data[[rowvar]]"
... Hello! I am not able to load my "ColData" (which contains information about my samples) on r and I am not sure why. I was able to load my "CountData" though. > countData <- as.matrix(read.csv(file.choose(), row.names = "gene_id")) > colData <- read.table(file.choose(),header=TR ...
R deseq2 rna-seq written 3 months ago by catglen0120 • updated 3 months ago by Kevin Blighe33k
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Comment: C: Prepare multiple gtf files for Ballgown
... Thank you for your help! ...
written 3 months ago by catglen0120
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Prepare multiple gtf files for Ballgown
... Hello! I want to run the following on my terminal: stringtie -e -B -p 8 -G stringtie_merged.gtf -o ballgown/ERR188044/ERR188044_chrX.gtf map/ERR188044_chrX.bam stringtie -e -B -p 8 -G stringtie_merged.gtf -o ballgown/ERR188104/ERR188104_chrX.gtf map/ERR188104_chrX.bam but I have many diff ...
hisat rna-seq hisat2 written 3 months ago by catglen0120
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Comment: C: Issue with DESeq2: Unable to create a DESeqDataSet because names in colData don'
... hello! I was able to resolve the issue by fixing how the colData is arranged. Thanks for the help nevertheless. ...
written 5 months ago by catglen0120
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Comment: C: Issue with DESeq2: Unable to create a DESeqDataSet because names in colData don'
... countData: gene_id Ceratodon_GG1 Ceratodon_R40 MSTRG.9134 3497 998 colData: ids sex Ceratodon_GG1 female ...
written 5 months ago by catglen0120

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