Hello everyone,
I did my transcripts count using Htseq and now I am trying to use DESeq2 package in R to see differential expression of genes around samples.In order to make the input table for Deseq2 I am using following line of codes:
directory <- C:/Users/hp/Desktop/RNA.seq.data
sampleFiles <- c('count.1','count.2','count.3','count.4','count.6','count.7','count.8')
sampleCondition<- c('R1control','R1time1','R1time2','R1time4','R2control','R2time1','R2time2','R2time4')
sampleTable<- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = sampleCondition)
ddsHTSeq<- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
directory = directory,
design= ~ condition)
ddsHTSeq
In the first line of code where I specify path to directory containing count files I always get syntax error. I tried everything like setting working directory and specifying path all that but this is not working. The R version I am using is 3.4.2.
Please Help.
Thank you,
Ambika
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Try either of these:
directory <- "C:\\Users\\hp\\Desktop\\RNA.seq.data\\"
directory <- "C:/Users\\hp/Desktop/RNA.seq.data/"
Ensure that you include the quotation marks
Thank you Kevin,
That worked and now I got another error in command
sampleTable<- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = sampleCondition)
Error in data.frame(sampleName = sampleFiles, fileName = sampleFiles, : arguments imply differing number of rows: 7, 8
Am I wrong somewhere?
Yes, I believe that you are missing a 'count.5' in your vector sampleFiles(?).
sampleFiles = 7 elements
sampleCondition = 8 elements
These have to be the same length and the order should match
Absolutely no problem my friend. Good luck
I always set the directory while reading the data file.
For example:
dat = read.csv( file = "/Users/zzzz/Desktop/matrix.csv", header = T, row.names=1)
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