Hello
my name is Ben. first time am using DESeq2 .
I have followed the vignette and obtained my summarisedExperiment output
> se
class: RangedSummarizedExperiment
dim: 35800 4
metadata(0):
assays(1): counts
rownames(35800): NM_001001130 NM_001001144 ... NR_148724 NR_148917
rowData names(0):
colnames: NULL
colData names(0):
colSums( assay(se) )
[1] 24889663 22774250 16492881 20492437
>
> c> olData(se)
DataFrame with 4 rows and 0 columns
> ## DataFrame with 3 rows and 0 columns
> bamLst
BamFileList of length 4
names(4): ko1.bam ko2.bam wt1.bam wt2.bam
How do i assign metadata to my 4 bam files;?
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] DESeq2_1.16.1 GenomicAlignments_1.12.2 SummarizedExperiment_1.6.3
[4] DelayedArray_0.2.7 matrixStats_0.52.2 Rsamtools_1.28.0
[7] Biostrings_2.44.2 XVector_0.16.0 GenomicFeatures_1.28.4
[10] AnnotationDbi_1.38.2 Biobase_2.36.2 GenomicRanges_1.28.4
[13] GenomeInfoDb_1.12.2 IRanges_2.10.2 S4Vectors_0.14.3
[16] BiocGenerics_0.22.0 BiocInstaller_1.26.0
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 Rcpp_0.12.12 lattice_0.20-35
[4] digest_0.6.12 plyr_1.8.4 backports_1.1.0
[7] acepack_1.4.1 RSQLite_2.0 ggplot2_2.2.1
[10] zlibbioc_1.22.0 rlang_0.1.2 lazyeval_0.2.0
[13] annotate_1.54.0 data.table_1.10.4 blob_1.1.0
[16] rpart_4.1-11 Matrix_1.2-11 checkmate_1.8.3
[19] splines_3.4.1 BiocParallel_1.10.1 geneplotter_1.54.0
[22] stringr_1.2.0 foreign_0.8-69 htmlwidgets_0.9
[25] RCurl_1.95-4.8 bit_1.1-12 biomaRt_2.32.1
[28] munsell_0.4.3 compiler_3.4.1 rtracklayer_1.36.4
[31] pkgconfig_2.0.1 base64enc_0.1-3 htmltools_0.3.6
[34] nnet_7.3-12 tibble_1.3.4 gridExtra_2.2.1
[37] htmlTable_1.9 GenomeInfoDbData_0.99.0 Hmisc_4.0-3
[40] XML_3.98-1.9 bitops_1.0-6 grid_3.4.1
[43] xtable_1.8-2 gtable_0.2.0 DBI_0.7
[46] magrittr_1.5 scales_0.4.1 stringi_1.1.5
[49] genefilter_1.58.1 latticeExtra_0.6-28 Formula_1.2-2
[52] RColorBrewer_1.1-2 tools_3.4.1 bit64_0.9-7
[55] survival_2.41-3 colorspace_1.3-2 cluster_2.0.6
[58] memoise_1.1.0 knitr_1.17
hi thanks for pointing me to the information. i have added column information as below
> condition <- factor(c("ko","ko","wt","wt")) > library("DESeq2") > ddsSE <- DESeqDataSet(se, design = ~ condition) Error in DESeqDataSet(se, design = ~condition) : all variables in design formula must be columns in colDatawhat could be causing this error ?
thanks
Benjy
Hello
thanks for the reply
I have added this column to the table and generated some graps!
> sampleTable Condition ko1 ko ko2 ko ko3 ko wt1 wt wt2 wt wt3 wt > colData(se) <- DataFrame(sampleTable) > colData(se) DataFrame with 6 rows and 1 column Condition <factor> ko1 ko ko2 ko ko3 ko wt1 wt wt2 wt wt3 wt > topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 20) > mat <- assay(rld)[ topVarGenes, ] > mat <- mat - rowMeans(mat) > anno <- as.data.frame(colData(rld)[, c("Condition")]) > pheatmap(mat, annotation_col = anno)Error in check.length("fill") :
'gpar' element 'fill' must not be length 0
what could be causing this error and why are my Poisson Distance heatmap not showing my sample names?
pheatmap is a CRAN package, so if you have questions about that, you need to ask on R-help (r-help@r-project.org).