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  • DESeq and data frame error

    Hello everyone,
    I’m new to R and DESeq2 and I’m excited to get already some results.
    I want to compare the gene expression of two conditions so I have 2 file.bam
    I used featureCounts to generate the count files and now I’m switching to DESEq2 in R for the identification of differentially expressed genes.

    The used command lines to load the input table created is:

    Code:
    > countdata <- as.matrix(read.table("DESeq2_STAR/CUTLL1.counts.table", header=TRUE, row.names=1))

    The first question is, if I have two count tables for the two conditions(CUTLL1.counts.table and KOPTK1.counts.table), do I have to use this command twice such as

    Code:
    > countdata <- as.matrix(read.table("DESeq2_STAR/CUTLL1.counts.table", header=TRUE, row.names=1))
    > countdata <- as.matrix(read.table("DESeq2_STAR/KOPTK1.counts.table", header=TRUE, row.names=1))
    I also tried this with no success

    [CODE]countdata <- as.matrix(read.table(c("DESeq2_STAR/CUTLL1.counts.table","DESeq2_STAR/KOPTK1.counts.table", header=TRUE, row.names=1 )))[CODE]


    Than I created a data frame

    Code:
    condition <- factor(c(rep("CUTLL1", 1), rep("KOPTK1", 1)))
    I assigned this two names for this two conditions CUTLL1 and KOPTK1 respectively and it was ok,

    At the end I got an error when I did set the condition,



    > coldata <- data.frame(row.names=colnames(countdata), condition)
    Error in data.frame(row.names = colnames(countdata), condition) :
    'row.names' should specify one of the variables


    Can you please tell me what’s wrong with that?
    I will appreciate any help,
    Thank you

    -P
    Last edited by NDUFB11; 02-21-2019, 10:04 AM.

  • #2
    ok I solved the problem by combining the two bam files with this command line,

    # Program:featureCounts v1.6.3; Command:"featureCounts" "-M" "--fraction" "-g" "gene_id" "-T" "4" "-s" "0" "-a" "annotation/Homo_sapiens.GRCh37.75.gtf" "-o" "counts/CUTLLandKOPTK.star.featureCounts" "mapping/star/KOPTK1_NSC.bam" "mapping/star/CUTLL1_NSC.bam"

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