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$clone, count.a.samples) :
invalid subscript type 'list'
Sample of pop.J.counts looks like this:
TranscriptName J1a J1b J1c J21a J21b J21c J24a J24b J24c J2a J2b J2c J3a J3b J3c J4a J4b J4c
1 aaa1 364 341 396 339 364 442 375 499 447 353 329 521 267 325 380 346 344 407
2 aaa2 1011 863 810 986 1051 972 992 1039 848 979 710 1132 725 1052 1122 887 849 1009
3 aaa3 109 65 73 61 93 86 100 80 81 82 81 68 69 92 117 94 96 96
4 aaa4 473 281 265 399 483 296 553 330 344 702 397 746 494 844 783 446 457 727
5 aaa5 0 1 0 2 0 1 2 0 0 0 0 3 0 2 3 0 1 0
6 aaa6 5 1 3 14 41 11 6 5 6 5 4 9 10 6 4 1 4 3
I am relatively new to RNA-seq analysis and I am trying to use DESeq for analyzing the count data. Through some pre-processing, I have already obtained the raw data counts from an RNA-seq experiment that has 6 clones and 3 biological replicates. I tried to imitate the DESeq vignette for my data using the following commands:
1. pop.J.counts <- read.table("PopJ.tab", sep='\t', stringsAsFactors=F, header=T))
2. pop.J.design <- data.frame(row.names=c("J1a","J1b","J1c","J21a","J21b","J21c","J24a","J24b","J24c","J2a","J2b","J2c","J3a","J3b","J3c","J4a","J4b","J4c"), clone=c("J1", "J1", "J1", "J21","J21","J21","J24","J24","J24", "J2","J2","J2", "J3","J3","J3", "J4","J4","J4"), replicate=c("a", "b", "c","a", "b", "c", "a", "b", "c", "a", "b", "c","a", "b", "c", "a", "b", "c"))
3. rep.a.samples = pop.J.design$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
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