DESeq2 Contrast

[Ruhi]

I want to use the contrast option in DESeq2

ddsctrst <- DESeq(ddsctrst)

ddsctrst
class: DESeqDataSet
dim: 133000 8
exptData(0):
assays(3): counts mu cooks
rownames(133000): comp0_c0 comp100000_c0 ... comp99998_c0 comp99999_c0
rowData metadata column names(36): baseMean baseVar ... maxCooks
cooksOutlier
colnames(8): ABC542 ABC4544 ... ABC4552 ABC4553
colData names(2): condition sizeFactor

head(colData(ddsctrst))DataFrame with 6 rows and 2 columns
condition sizeFactor
<factor> <numeric>
ABC4542 tmp1 1.8234436
ABC4544 tmp3 1.0633168
ABC4547 tmp2 0.4302194
ABC4548 tmp1 1.5796472
ABC4549 tmp2 1.2879635
ABC4551 tmp3 0.9606662

resultsNames(ddsctrst)

[1] "Intercept" "condition_tmp2_vs_tmp1" "condition_tmp3_vs_tmp1"
[4] "condition_tmp4_vs_tmp1"

I want to do this step

rstCtrst <- results(ddsctrst, contrast=c("condition","tmp1","tmp3"))
Error in results(ddsctrst, contrast = c("condition", "tmp1", "tmp3")) :
unused argument (contrast = c("condition", "tmp1", "tmp3"))

kindly provide some suggestion

[dpryan]

What's the output of

sessionInfo()

BTW, why not just:

rstCtrst <- results(ddsctrst, name="condition_tmp3_vs_tmp1")

That would seem to simply do exactly what you want.

[Ruhi]

I want to compare all the conditions among eachother and
resultsNames(ddsctrst)

[1] "Intercept" "condition_tmp2_vs_tmp1" "condition_tmp3_vs_tmp1"
[4] "condition_tmp4_vs_tmp1"

gives me only three options, how do I get a comparison for example between tmp2 vs tmp3

[dpryan]

Again, what is the output of "sessionInfo()"?

[Ruhi]

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] DESeq2_1.0.19 BiocInstaller_1.10.4 RcppArmadillo_0.4.200.0
[4] Rcpp_0.11.1 lattice_0.20-23 Biobase_2.20.1
[7] GenomicRanges_1.12.5 IRanges_1.18.3 BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] annotate_1.38.0 AnnotationDbi_1.22.6 DBI_0.2-7
[4] genefilter_1.42.0 grid_3.0.2 locfit_1.5-9.1
[7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2
[10] stats4_3.0.2 survival_2.37-4 tools_3.0.2
[13] XML_3.98-1.1 xtable_1.7-3

[dpryan]

That's a rather outdated version that your using. Contrasts appear to have been added in version 1.1.24 (you're using 1.0.19 and the current version is 1.4.0). You'll need to upgrade if you want to use contrasts (do upgrade to the most recent version, Michael Love made changes in it that would benefit you).

[Ruhi]

ok I will try that, thank you for your response and suggestions