Hello,

I have a small query regarding saving EISA results. After running the analysis, I am trying to get the csv file of the results, in order to know the genes that have been shown to be under post-transcriptional regulation. I used write.csv (...) command, which is resulting in an error. I have pasted below, the details of my analysis. Please guide me as to how to know the details of the genes (as a text/excel file), that are being shown as up/downregulated in the plot. Thanks a lot

sampleFile <- "samplefileETJA.txt" genomeFile <- "crov2asm.fasta"

proj <- qAlign(sampleFile = "samplefileETJA.txt", + genome = "crov2asm.fasta", + aligner = "Rhisat2", splicedAlignment = TRUE) alignment files missing - need to: create 3 genomic alignment(s) will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s Testing the compute nodes...OK Loading QuasR on the compute nodes...OK Available cores: DB9710C2: 1 Performing genomic alignments for 3 samples. See progress in the log file: C:/Users/smile/Documents\QuasRlog7ec5c234d68.txt Genomic alignments have been created successfully

alignmentStats(proj) seqlength mapped unmapped ControlA:genome 541127784 35259067 2048766 ControlB:genome 541127784 40804329 2240085 ControlC:genome 541127784 37599220 2029814 JasmonateA:genome 541127784 37638359 3051038 JasmonateB:genome 541127784 37207875 2061034 JasmonateC:genome 541127784 34827460 1881215 cntEx <- qCount(proj, regU$exons, orientation = "any") counting alignments...done collapsing counts by query name...done

cntGb <- qCount(proj, regU$genebodies, orientation = "any") counting alignments...done

cntIn <- cntGb - cntEx head(cntEx) width ControlA ControlB ControlC JasmonateA JasmonateB JasmonateC CRO100001 1214 37 68 87 118 72 58 CRO100002 545 0 0 0 0 0 0 CRO100003 514 0 0 0 0 0 0 CRO100004 805 10 10 2 4 6 8 CRO100006 1161 0 0 0 0 0 0 CRO100007 378 0 0 0 0 0 0

head(cntIn) width ControlA ControlB ControlC JasmonateA JasmonateB JasmonateC CRO100001 4187 12 21 17 14 20 16 CRO100002 1696 0 0 0 0 0 0 CRO100003 127 0 0 0 0 0 0 CRO100004 3285 0 0 1 2 0 2 CRO100006 816 0 0 0 0 0 0 CRO100007 928 0 0 0 0 0 0 saveRDS(cntEx, file = "ETandJAexonic.rds") saveRDS(cntIn, file = "ETandJAintronic.rds") cntEx <- readRDS("ETandJAexonic.rds") cntIn <- readRDS("ETandJAintronic.rds") Rex <- cntEx[, colnames(cntEx) != "width"] Rin <- cntIn[, colnames(cntIn) != "width"] cond <- factor(c("CK", "CK", "CK", "JA", "JA", "JA")) res <- runEISA(Rex, Rin, cond) Error in runEISA(Rex, Rin, cond) : could not find function "runEISA" library(eisaR) res <- runEISA(Rex, Rin, cond) filtering quantifyable genes...keeping 11460 from 27152 (42.2%) fitting statistical model...done calculating log-fold changes...done plotEISA(res) identified 159 genes to highlight write.csv(res, file=CKandJA_EISA.csv) Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : arguments imply differing number of rows: 0, 1 write.csv(res, file=CKandJA.csv, traitsAsDir = FALSE, csv2 = TRUE, row.names = FALSE) Error in write.table(res, file = CKandJA.csv, traitsAsDir = FALSE, csv2 = TRUE, : unused arguments (traitsAsDir = FALSE, csv2 = TRUE)

Session info:

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LCCOLLATE=EnglishIndia.1252 LCCTYPE=EnglishIndia.1252 LCMONETARY=EnglishIndia.1252 [4] LCNUMERIC=C LCTIME=English_India.1252

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

other attached packages: [1] eisaR1.1.1 QuasR1.29.4 Rbowtie1.29.1 GenomicRanges1.41.6 [5] GenomeInfoDb1.25.10 IRanges2.23.10 S4Vectors0.27.12 BiocGenerics0.35.4

loaded via a namespace (and not attached): [1] Biobase2.49.0 httr1.4.2 edgeR3.31.4
[4] splines4.0.2 bit644.0.4 GenomicFiles1.25.0
[7] assertthat0.2.1 askpass1.1 BiocManager1.30.10
[10] BiocFileCache1.13.1 latticeExtra0.6-29 blob1.2.1
[13] BSgenome1.57.6 GenomeInfoDbData1.2.3 Rsamtools2.5.3
[16] progress1.2.2 pillar1.4.6 RSQLite2.2.0
[19] lattice0.20-41 glue1.4.2 limma3.45.10
[22] digest0.6.25 RColorBrewer1.1-2 XVector0.29.3
[25] Matrix1.2-18 XML3.99-0.5 pkgconfig2.0.3
[28] ShortRead1.47.2 biomaRt2.45.2 zlibbioc1.35.0
[31] purrr0.3.4 jpeg0.1-8.1 BiocParallel1.23.2
[34] tibble3.0.3 openssl1.4.2 generics0.0.2
[37] ellipsis0.3.1 SummarizedExperiment1.19.6 GenomicFeatures1.41.2
[40] magrittr1.5 crayon1.3.4 memoise1.1.0
[43] hwriter1.3.2 tools4.0.2 prettyunits1.1.1
[46] hms0.5.3 lifecycle0.2.0 matrixStats0.56.0
[49] stringr1.4.0 locfit1.5-9.4 DelayedArray0.15.4
[52] AnnotationDbi1.51.3 Biostrings2.57.2 compiler4.0.2
[55] rlang0.4.7 grid4.0.2 RCurl1.98-1.2
[58] VariantAnnotation1.35.3 rappdirs0.3.1 bitops1.0-6
[61] DBI1.1.0 curl4.3 R62.4.1
[64] GenomicAlignments1.25.3 dplyr1.0.2 rtracklayer1.49.5
[67] bit4.0.4 stringi1.4.6 Rcpp1.0.5
[70] vctrs0.3.3 png0.1-7 dbplyr1.4.4
[73] tidyselect_1.1.0

The res object is not a data.frame, but a list containing several different types of information (see ?runEISA). You want to extract the result table (res$tab.ExIn) and write that to a file.