This is my first question in Bioconductor support and I am completely new to R and bioinformatics, so I apologize if the reply to my question seems obvious.
I am trying to compare RNA-seq data of two different conditions: LG (5 replicates) vs HG (3 replicates) by using RUVSeq to remove unwanted variation between batches.
The data look like this: The columns are the samples: HG1,HG2,HG3,HG5,HG4,LG1,LG2,LG5 The rows are the genes: NM000014, NM000015... up to 18000 genes.
The code I wrote is the following:
count_tab <- read.table("Human_islets_counts_Refseq_HG_vs_LG.csv",header = TRUE,row.names = 1,sep = ',') filter <- apply(count_tab, 1, function(x) length(x[x>5])>=2) filtered <- count_tab[filter,] genes <- rownames(filtered)[grep("^NM", rownames(filtered))] x <- as.factor(rep(c("HG", "LG"), each=5,3)) set <- newSeqExpressionSet(as.matrix(filtered),phenoData = data.frame(x, row.names=colnames(filtered))) Error in data.frame(x, row.names = colnames(filtered)) : row names supplied are of the wrong length
Anyone could give me a hint on why this is wrong?
Thanks in advance Cecilia
> sessionInfo() R version 3.6.0 alpha (2019-04-08 r76348) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252  LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  RUVSeq_1.17.1 edgeR_3.25.4 limma_3.39.15 EDASeq_2.17.4  ShortRead_1.41.0 GenomicAlignments_1.19.1 SummarizedExperiment_1.13.0 DelayedArray_0.9.9  matrixStats_0.54.0 Rsamtools_1.99.6 GenomicRanges_1.35.1 GenomeInfoDb_1.19.3  lattice_0.20-38 locfit_1.5-9.1 zebrafishRNASeq_1.3.0 Biostrings_2.51.5  XVector_0.23.2 IRanges_2.17.5 S4Vectors_0.21.23 BiocParallel_1.17.18  Biobase_2.43.1 BiocGenerics_0.29.2 loaded via a namespace (and not attached): Error in x[["Version"]] : subscript out of bounds In addition: Warning messages: 1: In FUN(X[[i]], ...) : DESCRIPTION file of package 'RCurl' is missing or broken 2: In FUN(X[[i]], ...) : DESCRIPTION file of package 'bitops' is missing or broken