Thread: DESeq2 Error
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Old 01-26-2015, 12:52 PM   #1
nw328
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Location: DC

Join Date: Jan 2015
Posts: 4
Default DESeq2 Error

Hi All,
I am trying to use DESeq2 to analyze some RNAseq count data from a .csv. It is an experiment with 5 conditions done in duplicate (WT, null, condition1, condition2, condition3) . I am relatively new to R, and have been primarily borrowing snippets of applicable scripts, largely from this thread. Here is what I have so far:



>library(ggplot2)
>library(DESeq2)
>library(Biobase)

>df<-read.csv('/Volumes/NICK3/R/data/RNAseq_sandbox.csv', header=T, sep=",", row.names=1)

>countsTable <-data.matrix(df[1:10], rownames.force = NA)
> head(countsTable)
# WT_a WT_b null_a null_b test1_a test1_b test2_a test2_b test3_a test3_b
#s00010 6293 8602 4339 6691 4614 8632 4093 8830 7656 9657
#s00020 4009 6370 2647 4488 3001 6044 2586 5885 5441 6468
#s00030 858 1413 624 1122 684 1220 648 1452 1170 1276
#s00040 5350 8466 4354 7175 4106 8349 4329 8047 7283 7729
#s00050 666 1033 448 884 446 1030 453 980 829 1157
#s00060 11259 12059 8609 9902 8496 11568 8281 12140 10827 11676

>conditions<-c("X1", "X2", "A1", "A2", "B1", "B2", "C1", 'C2', "D1", "D2")
>samples <- data.frame(row.names=conditions, condition=as.factor(c(rep("ctl",2), rep("test",8))))
> samples
# condition
#X1 ctl
#X2 ctl
#A1 test
#A2 test
#B1 test
#B2 test
#C1 test
#C2 test
#D1 test
#D2 test

dds <- DESeqDataSetFromMatrix(countData = countsTable, colData=samples, design=~condition)
#Error in if (any(assay(se) < 0)) { :
# missing value where TRUE/FALSE needed


I am a little unsure of where to go from here with this error. I dont have null values or negatives. It seems that I am not giving the right syntax for making the summarizedExperiment.

Any help would be appreciated; thanks in advance!
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