Problems with compareAgainstL1000

[fransilvion]

Hi,

for some reason, when I am running the same code from this pdf, when I execute the line:

compareSmallMolecule$spearman <- compareAgainstL1000( diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="spearman")

I am getting the following error:

Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed

What might be the problem?

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

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

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

other attached packages:
[1] dplyr_0.7.8 cTRAP_1.0.2 biomaRt_2.38.0 Biobase_2.42.0 BiocGenerics_0.28.0 DeMAND_1.12.0
[7] KernSmooth_2.23-15 limma_3.38.2

loaded via a namespace (and not attached):
[1] httr_1.3.1 jsonlite_1.5 bit64_0.9-7 R.utils_2.7.0 gtools_3.8.1
[6] assertthat_0.2.0 stats4_3.5.1 blob_1.1.1 yaml_2.2.0 progress_1.2.0
[11] slam_0.1-43 pillar_1.3.0 RSQLite_2.1.1 lattice_0.20-35 glue_1.3.0
[16] digest_0.6.18 colorspace_1.3-2 cowplot_0.9.3 Matrix_1.2-14 R.oo_1.22.0
[21] plyr_1.8.4 XML_3.98-1.16 pkgconfig_2.0.2 purrr_0.2.5 relations_0.6-8
[26] scales_1.0.0 gdata_2.18.0 BiocParallel_1.16.0 tibble_1.4.2 IRanges_2.16.0
[31] ggplot2_3.1.0 pbapply_1.3-4 lazyeval_0.2.1 magrittr_1.5 crayon_1.3.4
[36] memoise_1.1.0 R.methodsS3_1.7.1 gplots_3.0.1 tools_3.5.1 data.table_1.11.8
[41] prettyunits_1.0.2 hms_0.4.2 stringr_1.3.1 Rhdf5lib_1.4.0 S4Vectors_0.20.1
[46] munsell_0.5.0 cluster_2.0.7-1 AnnotationDbi_1.44.0 bindrcpp_0.2.2 compiler_3.5.1
[51] caTools_1.17.1.1 rlang_0.3.0.1 rhdf5_2.26.0 grid_3.5.1 RCurl_1.95-4.11
[56] marray_1.60.0 igraph_1.2.2 bitops_1.0-6 gtable_0.2.0 curl_3.2
[61] DBI_1.0.0 sets_1.0-18 R6_2.3.0 gridExtra_2.3 knitr_1.20
[66] bit_1.1-14 bindr_0.1.1 fastmatch_1.1-0 fgsea_1.8.0 readr_1.1.1
[71] stringi_1.2.4 Rcpp_1.0.0 piano_1.22.0 tidyselect_0.2.5

[fransilvion]

Also, when I run this line:
compareSmallMolecule$gsea <- compareAgainstL1000( diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="gsea", geneSize = 150)

I have a lot of warnings:

the condition has length > 1 and only the first element will be used

What exactly it means and how bad is it for following analysis? Thanks

[nuno-agostinho]

Hello @fransilvion, I just tried to run the tutorial again and everything is working fine.

Could you save your R environment in a RDS file and send it to me so I can analyse it? Please attach the RDS file in this thread or send it to me by email ([email protected]). Thank you!

[fransilvion]

Hi @nuno-agostinho, thanks for quick response! I tried to run tutorial again, and it worked, but for my own data set I still have this error. I can send you my diffExprStat file via email. I am searching for compounds in MCF7 cell line, and all other steps are the same as in tutorial.

[nuno-agostinho]

Hey @fransilvion, sorry for the delay in answering! Could you try to run the following commands?

library(cTRAP)
diffExprStat <- readRDS("diffExprStat.Rds")

# Summarise available conditions for CMap perturbations ------------------------
cellLine <- "MCF7"
l1000metadata <- downloadL1000data("l1000metadata.txt", "metadata")
l1000metadataSmallMolecules <- filterL1000metadata(
    l1000metadata, cellLine=cellLine, perturbationType="Compound")
getL1000conditions(l1000metadataSmallMolecules)

# Load compound-associated perturbations related to MCF7 cell line -------------
l1000zscores  <- downloadL1000data("l1000zscores.gctx", "zscores",
                                   l1000metadataSmallMolecules$sig_id)
l1000geneInfo <- downloadL1000data("l1000geneInfo.txt", "geneInfo")
l1000perturbationsSmallMolecules <- loadL1000perturbations(
    l1000metadataSmallMolecules, l1000zscores, l1000geneInfo)

# Compare against CMap perturbations -------------------------------------------
gseaResults <- compareAgainstL1000(
    diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="gsea",
    geneSize=150)

# Order based on similarity ----------------------------------------------------
gseaRes_ordered <- gseaRes[order(gseaRes$MCF7_WTCS, decreasing=TRUE), ]

head(gseaRes_ordered)
tail(gseaRes_ordered)

This should run with no issues and return the similar perturbations as tested in the MCF7 cell line from CMap. How does your script deviates from the one above?