DESeq: invalid subscript type 'list'

[biobudhan]

Hi All,
I am relatively new to RNA-seq analysis and I am trying to use DESeq for analyzing the count data. Through some pre-processing, I have already obtained the raw data counts from an RNA-seq experiment that has 6 clones and 3 biological replicates. I tried to imitate the DESeq vignette for my data using the following commands:

1. pop.J.counts <- read.table("PopJ.tab", sep='\t', stringsAsFactors=F, header=T))
2. pop.J.design <- data.frame(row.names=c("J1a","J1b","J1c","J21a","J21b","J21c","J24a","J24b","J24c","J2a","J2b","J2c","J3a","J3b","J3c","J4a","J4b","J4c"), clone=c("J1", "J1", "J1", "J21","J21","J21","J24","J24","J24", "J2","J2","J2", "J3","J3","J3", "J4","J4","J4"), replicate=c("a", "b", "c","a", "b", "c", "a", "b", "c", "a", "b", "c","a", "b", "c", "a", "b", "c"))
3. rep.a.samples = pop.J.design$replicate=="a"
4. count.a.samples = pop.J.counts[,rep.a.samples]
5. cond.a.samples = subset(pop.J.design$clone[count.a.samples])

However, I get the following error when I run the 5th step.:
Error in `[.default`(pop.J.design$clone, count.a.samples) :
invalid subscript type 'list'

Sample of pop.J.counts looks like this:
TranscriptName J1a J1b J1c J21a J21b J21c J24a J24b J24c J2a J2b J2c J3a J3b J3c J4a J4b J4c
1 aaa1 364 341 396 339 364 442 375 499 447 353 329 521 267 325 380 346 344 407
2 aaa2 1011 863 810 986 1051 972 992 1039 848 979 710 1132 725 1052 1122 887 849 1009
3 aaa3 109 65 73 61 93 86 100 80 81 82 81 68 69 92 117 94 96 96
4 aaa4 473 281 265 399 483 296 553 330 344 702 397 746 494 844 783 446 457 727
5 aaa5 0 1 0 2 0 1 2 0 0 0 0 3 0 2 3 0 1 0
6 aaa6 5 1 3 14 41 11 6 5 6 5 4 9 10 6 4 1 4 3

[Michael Love]

Hi,

A tip on R functions, whenever you have a problem, read the documentation for the function that gave an error.

Type ?subset, and read over the whole thing.

The arguments section is useful, as is the Usage section, and the Examples.

Also, we recommend users switch to DESeq2, as this is the supported version. You can read the vignette by typing:

library(DESeq2)
vignette("DESeq2")

and also you might check our workflow, which is designed for people who might be new to R:

http://bioconductor.org/help/workflows/rnaseqGene/