Question: Perform differential expression for illumina data
0
gravatar for Agaz Hussain Wani
5 weeks ago by
India
Agaz Hussain Wani40 wrote:

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
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Agaz Hussain Wani40

I doubt the data is not of correct format

Famous last words... It seems from the error you've presented, there's something amiss with your selDataMatrix object. Useful commands to try out:

  • str(selDataMatrix) - Structure of your object dim(selDataMatrix)
  • Dimensions of your object

I'm assuming you've omitted how you made the f object by mistake, but that would raise a different error to the one seen.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by andrew.j.skelton733.9k

Kindly follow the edit

ADD REPLYlink written 5 weeks ago by Agaz Hussain Wani40

Put in the results of:

head(selDataMatrix)

head(design)

ADD REPLYlink written 5 weeks ago by andrew.j.skelton733.9k

Please follow edit_2

ADD REPLYlink written 5 weeks ago by Agaz Hussain Wani40

Strange, It could be a namespace problem. Try: fit <- limma::lmFit(selDataMatrix, design)

ADD REPLYlink written 5 weeks ago by andrew.j.skelton733.9k

No luck... same error

ADD REPLYlink written 5 weeks ago by Agaz Hussain Wani40

Try explicit parameterisation: fit <- limma::lmFit(object = selDataMatrix, design = design)

ADD REPLYlink written 5 weeks ago by andrew.j.skelton733.9k

Same, no luck again.

ADD REPLYlink written 5 weeks ago by Agaz Hussain Wani40

Can you amend your post with sessionInfo()

ADD REPLYlink written 5 weeks ago by andrew.j.skelton733.9k

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.

ADD REPLYlink written 5 weeks ago by andrew.j.skelton733.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 962 users visited in the last hour