User: ccheung

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Posts by ccheung

<prev • 8 results • page 1 of 1 • next >
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Answer: A: edgeR: non-unique values when setting 'row.names' - but the row names are uniqu
... Hi, Haha, OK, I'm absolutely positive that the column names are not duplicated. With regard to your last comment, in fact, that is what I had input....Perhaps that is the problem. I will put in another command according to the edgeR vignette and see if that'll fix it.  Thanx! carol carol ...
written 4.6 years ago by ccheung0
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Answer: A: edgeR: non-unique values when setting 'row.names' - but the row names are uniqu
... Hi, Thanx John for your answer!  However, I double-checked and I am pretty sure that both the column and the row names are unique.  Just to be sure, I even put in the command, rownames(df) = make.names(nams, unique=TRUE) but to no avail..... Any other ideas? Thanx.   carol   ...
written 4.6 years ago by ccheung0
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edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
... Hi, I'm having problems with the DGEList function in edgeR.  Here are the commands that I had input: library(edgeR) raw.data <- read.table(file = "Documents/.../myfile.csv", header=TRUE, sep=",") Data <- raw.data[, 2:45] rownames( Data ) <- raw.data[ , 1 ] colnames(Data) <- paste (c("M ...
edger row.names dgelist written 4.6 years ago by ccheung0
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deseq: all padj values equal to 1
... Hi Everybody, I performed a deseq analysis on my samples (11 controls and 33 experimental samples). It is true that there are huge variations within each group, but although the pval are very low, the padj are always 1.  Plus when I put in the command: resSig = res[ res$padj <.05,] the list th ...
deseq padj written 4.7 years ago by ccheung0 • updated 4.4 years ago by Michael Love25k
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Answer: A: DESeq: filter out low count reads
... Thank you Michael! ...
written 4.7 years ago by ccheung0
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DESeq: filter out low count reads
... Hi Everybody, I 44 samples and >76000 transcripts in my RNA Seq data which was counted using FeatureCounts. I'd like to reduce the number of transcripts by filtering out the transcripts in which 80% of the samples (35 samples) have >10 reads. Can anyone suggest how I may do so? Thanx. car ...
deseq reads filter written 4.7 years ago by ccheung0
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Answer: A: Redundant meta-features (genes) using FeatureCounts
... Thanx Gordon! ...
written 4.7 years ago by ccheung0
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Redundant meta-features (genes) using FeatureCounts
... Hi, I'm completely new to RNASeq analysis so I'm having a lot of difficulties analyzing the data. First of all, I got some raw FeatureCount data, and there are multiple entries of the same meta-feature (gene) all with the same or very similar counts. What does this mean?  How do I combine them or r ...
featurecounts rna-seq written 4.7 years ago by ccheung0

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!

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