Hello, I have the output of HtSeq (=count tables as .txt files) as input for R and want to use arrayQualityMetrics. Is this somehow possible? I found this in the vignette: "If you are working on one colour arrays other than Affymetrix genechips, you can load your data into Bioconductor as an ExpressionSetobject, or if you work with Illumina data and the beadarray package, as an ExpressionSetIllumina object"

I have no idea if it is possible to receive either an ExpressionSetobject or an ExpressionSetIllumina object.

count_table <- read.table("all_counts_merged2.txt", header = TRUE)"
head(count_table)
#                  id   C     T1    T2   T3
# 1 rna-XM_011330573.3    0     0     0     0
# 2 rna-XM_011330574.2    0     0     0     0
# 3 rna-XM_011330575.3    0     0     0     0
# 4 rna-XM_011330577.3    0     0     0     0
# 5 rna-XM_011330578.3  133   374   382   246
# 6 rna-XM_011330579.3    0     0     0     0

I also generated a count Matrix:

countMatrix <- as.matrix(count_table[2:5]) 
rownames(countMatrix) <- count_table$id
head(countMatrix)
#                                 id   C     T1    T2   T3 
# rna-XM_011330573.3    0     0     0     0
# rna-XM_011330574.2    0     0     0     0
# rna-XM_011330575.3    0     0     0     0
# rna-XM_011330577.3    0     0     0     0
# rna-XM_011330578.3  133   374   382   246
# rna-XM_011330579.3    0     0     0     0

PS: I handle time course data (at the moment only one replicate) C=0 h, T1=24h, T2=48h, T3=120h (h=hours)

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] genefilter_1.66.0           gridExtra_2.3               RColorBrewer_1.1-2          pheatmap_1.0.12             limma_3.40.2                gplots_3.0.1.1             
 [7] arrayQualityMetrics_3.40.0  ggplot2_3.2.0               DESeq2_1.24.0               SummarizedExperiment_1.14.0 DelayedArray_0.10.0         BiocParallel_1.17.18       
[13] matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0        GenomeInfoDb_1.20.0         IRanges_2.18.1              S4Vectors_0.22.0           
[19] BiocGenerics_0.30.0        

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 von Paket 'rlang' fehlt oder zerstört
2: In FUN(X[[i]], ...) : DESCRIPTION von Paket 'dplyr' fehlt oder zerstört
3: In FUN(X[[i]], ...) :
  DESCRIPTION von Paket 'beadarray' fehlt oder zerstört