How to give directory path in DESeq2

Question

[AP]

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

Answer 1

[Kevin Blighe]

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

[AP]

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?

[Kevin Blighe]

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

[AP]

Thank you so much Kevin.

[Kevin Blighe]

Absolutely no problem my friend. Good luck

Answer 2

[Yuyayuya]

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)