Entering edit mode
7.3 years ago
AHW
▴
90
I am trying to perform differential expression of illumina data by using limma R package, but it gives an error
is.data.frame: argument "x" is missing, with no default
the code used is shown below
x.lumi <- lumiR(file)
lumiExpr <- lumiExpresso(x.lumi, bg.correct = TRUE, normalize = TRUE, verbose = TRUE)
dataMatrix <- exprs(lumiExpr)
presentCount <- detectionCall(lumiExpr)
selDataMatrix <- dataMatrix[presentCount > 0,]
probeList <- rownames(selDataMatrix)
design <- model.matrix(~0 + f)
colnames(design) <- unique
fit <- lmFit(selDataMatrix, design) ## error comes at this line
The sample of the data is
ID_REF 5522887032_E.AVG_Signal 5522887032_E.Avg_NBEADS 5522887032_E.BEAD_STDERR 5522887032_E.Detection Pval 5522887032_F.AVG_Signal 5522887032_F.Avg_NBEADS 5522887032_F.BEAD_STDERR 5522887032_F.Detection Pval 5522887032_I.AVG_Signal 5522887032_I.Avg_NBEADS 5522887032_I.BEAD_STDERR 5522887032_I.Detection Pval 5522887032_J.AVG_Signal 5522887032_J.Avg_NBEADS 5522887032_J.BEAD_STDERR 5522887032_J.Detection Pval 5455178010_A.AVG_Signal 5455178010_A.Avg_NBEADS 5455178010_A.BEAD_STDERR 5455178010_A.Detection Pval 5455178010_B.AVG_Signal 5455178010_B.Avg_NBEADS 5455178010_B.BEAD_STDERR 5455178010_B.Detection Pval 5455178010_E.AVG_Signal 5455178010_E.Avg_NBEADS 5455178010_E.BEAD_STDERR 5455178010_E.Detection Pval 5455178010_F.AVG_Signal 5455178010_F.Avg_NBEADS 5455178010_F.BEAD_STDERR 5455178010_F.Detection Pval 5455178010_I.AVG_Signal 5455178010_I.Avg_NBEADS 5455178010_I.BEAD_STDERR 5455178010_I.Detection Pval 5455178010_J.AVG_Signal 5455178010_J.Avg_NBEADS 5455178010_J.BEAD_STDERR 5455178010_J.Detection Pval
ILMN_1762337 89.86488 31 3.811882 0.2688312 163.4452 14 18.80181 0 82.05317 14 4.294791 0.7220779 138.5157 17 11.15551 0.005194805 124.2876 24 5.172565 0.2064935 159.7212 19 9.092192 0.005194805 107.3145 30 5.005895 0.2857143 190.262 20 19.90755 0 115.3796 30 4.957191 0.374026 200.1683 17 15.36981 0
ILMN_2055271 115.6802 17 12.9485 0.009090909 97.23217 12 3.956992 0.2519481 106.0408 19 6.191406 0.03636364 132.3083 21 7.402024 0.007792208 139.9317 21 8.396618 0.03896104 160.8593 18 11.53286 0.005194805 114.4995 25 4.781556 0.138961 119.8016 23 5.450975 0.05194805 142.8275 18 7.727149 0.01948052 148.5468 26 8.644123 0.02597403
I doubt the data is not of correct format. What is going wrong?? How I can perform differential expression??
EDIT
str(selDataMatrix)
num [1:18361, 1:10] 6.97 7.24 6.86 8 7.09 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:18361] "ILMN_1762337" "ILMN_2055271" "ILMN_1705025" "ILMN_1745607" ...
..$ : chr [1:10] "5522887032_E" "5522887032_F" "5522887032_I" "5522887032_J" ...
NULL
NULL
dim(selDataMatrix)
[1] 18361 10
EDIT_2
head(selDataMatrix)
5522887032_E 5522887032_F 5522887032_I 5522887032_J 5455178010_A 5455178010_B 5455178010_E 5455178010_F 5455178010_I 5455178010_J
ILMN_1762337 6.965474 7.495057 6.796738 7.310348 7.017493 7.414334 6.978447 7.833379 6.941810 7.571193
ILMN_2055271 7.237331 6.977815 7.138752 7.258688 7.173793 7.429328 7.058123 7.168598 7.200671 7.204627
ILMN_1705025 6.859176 6.777614 6.930740 7.329392 6.974015 6.874024 7.244121 7.110172 6.937978 7.108304
ILMN_1745607 8.004834 8.759304 7.637666 7.497618 8.002127 9.008094 7.907968 8.511522 7.548616 7.614281
ILMN_1735045 7.091717 6.999463 6.924700 6.747091 7.355837 6.762330 7.026471 6.763178 7.760299 7.278085
ILMN_1680754 7.300934 7.177784 7.014514 7.221381 6.973671 7.238551 7.004182 7.186080 7.011595 6.853043
head(design)
A B
1 1 0
2 0 1
3 1 0
EDIT_3
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
locale:
[1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8
[6] LC_MESSAGES=en_IN.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] tools stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] gtools_3.5.0 affyio_1.42.0 dtplyr_0.0.1 tibble_1.1 hwgcod.db_3.4.0 h10kcod.db_3.4.0
[7] h20kcod.db_3.4.0 org.Hs.eg.db_3.3.0 AnnotationDbi_1.34.4 lumi_2.24.0 codelink_1.40.2 limma_3.28.21
[13] dplyr_0.5.0 data.table_1.9.6 plyr_1.8.4 markdown_0.7.7 oligo_1.36.1 Biostrings_2.40.2
[19] XVector_0.12.1 IRanges_2.6.1 S4Vectors_0.10.3 oligoClasses_1.34.0 simpleaffy_2.48.0 gcrma_2.44.0
[25] genefilter_1.54.2 affy_1.50.0 Biobase_2.32.0 BiocGenerics_0.18.0 shinyjs_0.9.1 shiny_0.13.2
loaded via a namespace (and not attached):
[1] nlme_3.1-131 bitops_1.0-6 matrixStats_0.51.0 RColorBrewer_1.1-2 httr_1.2.1
[6] GenomeInfoDb_1.8.7 doRNG_1.6 nor1mix_1.2-2 R6_2.1.3 KernSmooth_2.23-15
[11] lazyeval_0.2.0 DBI_0.5 mgcv_1.8-16 colorspace_1.2-6 methylumi_2.18.2
[16] base64_2.0 bit_1.1-12 preprocessCore_1.34.0 chron_2.3-47 pkgmaker_0.22
[21] rtracklayer_1.32.2 quadprog_1.5-5 stringr_1.1.0 digest_0.6.10 Rsamtools_1.24.0
[26] illuminaio_0.14.0 siggenes_1.46.0 GEOquery_2.38.4 htmltools_0.3.5 RSQLite_1.0.0
[31] BiocInstaller_1.22.3 jsonlite_1.1 mclust_5.2 BiocParallel_1.6.6 RCurl_1.95-4.8
[36] magrittr_1.5 Matrix_1.2-7.1 Rcpp_0.12.6 stringi_1.1.1 nleqslv_3.0.3
[41] MASS_7.3-45 SummarizedExperiment_1.2.3 zlibbioc_1.18.0 bumphunter_1.12.0 grid_3.3.3
[46] affxparser_1.44.0 minfi_1.18.6 miniUI_0.1.1 lattice_0.20-34 splines_3.3.3
[51] multtest_2.28.0 GenomicFeatures_1.24.5 annotate_1.50.1 locfit_1.5-9.1 beanplot_1.2
[56] GenomicRanges_1.24.3 rngtools_1.2.4 codetools_0.2-15 biomaRt_2.28.0 XML_3.98-1.5
[61] httpuv_1.3.3 foreach_1.4.3 openssl_0.9.4 reshape_0.8.6 assertthat_0.1
[66] mime_0.5 xtable_1.8-2 ff_2.2-13 survival_2.40-1 iterators_1.0.8
[71] GenomicAlignments_1.8.4 registry_0.3
Famous last words... It seems from the error you've presented, there's something amiss with your
selDataMatrixobject. Useful commands to try out:str(selDataMatrix)- Structure of your objectdim(selDataMatrix)I'm assuming you've omitted how you made the
fobject by mistake, but that would raise a different error to the one seen.Kindly follow the edit
Put in the results of:
head(selDataMatrix)head(design)Please follow edit_2
Strange, It could be a namespace problem. Try:
fit <- limma::lmFit(selDataMatrix, design)No luck... same error
Try explicit parameterisation:
fit <- limma::lmFit(object = selDataMatrix, design = design)Same, no luck again.
Can you amend your post with
sessionInfo()Limma is currently at version 3.32.5, and R is at version 3.4.1. I'd consider updating, this might be the reason for your issues.