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Question: Error in 'colnames' while running case 1 of TCGABiolinks
0
gravatar for zeeniajagga
22 months ago by
zeeniajagga0 wrote:

I am trying to reproduce case 1 from TCGA Biolinks which is Pan Cancer downstream analysis BRCA from https://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html#case-study-n.-1-pan-cancer-downstream-analysis-brca and getting an error in dataprep step 

Error in `colnames<-`(`*tmp*`, value = c("TCGA-EB-A51B-01A-11R-A27Q-07",  : 

length of 'dimnames' [2] not equal to array extent

This case runs through following commands

>library(TCGAbiolinks) 

>cancer <- "BRCA"

>PlatformCancer <- "IlluminaHiSeq_RNASeqV2"

>dataType <- "rsem.genes.results"

>pathCancer <- paste0("../data",cancer)

>datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3")

>lsSample <- TCGAquery_samplesfilter(query = datQuery)

>dataSubt <- TCGAquery_subtype(tumor = cancer)

>dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample = "TP") >dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample ="NT")

>dataClin <- TCGAquery_clinic(tumor = cancer, clinical_data_type = "clinical_patient") TCGAdownload(data >datQuery, path = pathCancer, type = dataType, samples = c(dataSmTP,dataSmTN))

>dataAssy <- TCGAprepare(query = datQuery, dir = pathCancer, type = dataType, save = TRUE, >summarizedExperiment = TRUE, samples = c(dataSmTP,dataSmTN), filename paste0(cancer,"_",PlatformCancer,".rda")) 

##Till here, all the commands runs smooth and in the next step of data prep where is error in 'colnames'

> dataPrep <- TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)
Error in `colnames<-`(`*tmp*`, value = c("TCGA-EB-A51B-01A-11R-A27Q-07",  : 
length of 'dimnames' [2] not equal to array extent

Below is the session information and I would really appreciate any help to troubleshoot this.

> sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] SummarizedExperiment_1.0.2 Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
[5] IRanges_2.4.6              S4Vectors_0.8.11           BiocGenerics_0.16.1        TCGAbiolinks_1.0.5        

 

ADD COMMENTlink modified 22 months ago • written 22 months ago by zeeniajagga0
1
gravatar for tiagochst
22 months ago by
tiagochst100
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
tiagochst100 wrote:

I ran the same code below (case #1)  in OS X and I got no error. It might be something related to windows, I'll test on windows. 

But, just to know, your  dataAssy object gives the exact same output as below?

 

 

> dataAssy

class: RangedSummarizedExperiment 

dim: 20330 1211 

metadata(3): Query: TCGAprepareParameters FilesInfo:

assays(2): raw_counts scaled_estimate

rownames(20330): A1BG|1 A1CF|29974 ... ZZEF1|23140 ZZZ3|26009

rowRanges metadata column names(3): gene_id entrezgene

  transcript_id.transcript_id_TCGA-E9-A1RD-11A-33R-A157-07

colnames(1211): TCGA-E9-A1RD-11A-33R-A157-07

  TCGA-E9-A1RC-01A-11R-A157-07 ... TCGA-D8-A1J9-01A-11R-A13Q-07

  TCGA-AC-A6IX-01A-12R-A32P-07

colData names(10): sample patient ... Siglust PAM50
> dataPrep <- TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)


> sessionInfo()

R version 3.2.3 (2015-12-10)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.11.3 (El Capitan)


locale:

[1] pt_BR.UTF-8/pt_BR.UTF-8/pt_BR.UTF-8/C/pt_BR.UTF-8/pt_BR.UTF-8


attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     


other attached packages:

[1] TCGAbiolinks_1.0.5         SummarizedExperiment_1.0.2

[3] Biobase_2.30.0             GenomicRanges_1.22.4      

[5] GenomeInfoDb_1.6.3         IRanges_2.4.7             

[7] S4Vectors_0.8.11           BiocGenerics_0.16.1       
ADD COMMENTlink modified 22 months ago • written 22 months ago by tiagochst100
0
gravatar for zeeniajagga
22 months ago by
zeeniajagga0 wrote:

dataAssy object is giving me the exact same output as in your case, though I am getting some warnings in the previous steps and error in colnames..I have pasted the complete session output below.

> library(TCGAbiolinks)
Warning messages:
1: replacing previous import by ‘grid::arrow’ when loading ‘TCGAbiolinks’
2: replacing previous import by ‘grid::unit’ when loading ‘TCGAbiolinks’
> library(SummarizedExperiment)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall,
    clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB,
    parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame,
    as.vector, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get,
    grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames,
    sapply, setdiff, sort, table, tapply, union,
    unique, unlist, unsplit

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material;
    view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and
    for packages 'citation("pkgname")'.

> library(TCGAbiolinks)
> 
> cancer <- "BRCA"
> PlatformCancer <- "IlluminaHiSeq_RNASeqV2"
> dataType <- "rsem.genes.results"
> pathCancer <- paste0("../data",cancer)
> 
> datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3")
> lsSample <- TCGAquery_samplesfilter(query = datQuery)
> 
> # get subtype information
> dataSubt <- TCGAquery_subtype(tumor = cancer)
> 
> # Which samples are Primary Solid Tumor
> dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample = "TP")
> 
> # Which samples are Solid Tissue Normal
> dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample ="NT")
> 
> # get clinical data
> dataClin <- TCGAquery_clinic(tumor = cancer, clinical_data_type = "clinical_patient")
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:1 files
| Path:./nationwidechildrens.org_BRCA.bio.Level_2.0.42.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |=============================================| 100%
Tumor type: BRCA
  |                                             |   0%
Adding disease collumn to data frame
> 
> TCGAdownload(data = datQuery,
+              path = pathCancer,
+              type = dataType,
+              samples = c(dataSmTP,dataSmTN))
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:1211 files
| Path:../dataBRCA/unc.edu_BRCA.IlluminaHiSeq_RNASeqV2.Level_3.1.11.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |=============================================| 100%
> 
> dataAssy <- TCGAprepare(query = datQuery,
+                         dir = pathCancer,
+                         type = dataType,
+                         save = TRUE,
+                         summarizedExperiment = TRUE,
+                         samples = c(dataSmTP,dataSmTN),
+                         filename = paste0(cancer,"_",PlatformCancer,".rda"))
  |=============================================================================================================| 100%
Adding metadata to the rse object...
Saving the data...
Data saved in: BRCA_IlluminaHiSeq_RNASeqV2.rda
Warning messages:
1: In fread(files[i], header = TRUE, sep = "\t", stringsAsFactors = FALSE) :
  Stopped reading at empty line 14607 but text exists afterwards (discarded): RALA|589
2: In data.table::data.table(...) :
  Item 2 is of size 14605 but maximum size is 20531 (recycled leaving remainder of 5926 items)
3: In fread(files[i], header = TRUE, sep = "\t", stringsAsFactors = FALSE) :
  Stopped reading at empty line 2346 but text exists afterwards (discarded): C21orf57|54059    500.0
4: In data.table::data.table(...) :
  Item 2 is of size 2344 but maximum size is 20531 (recycled leaving remainder of 1779 items)
> 
> dataAssy
class: RangedSummarizedExperiment 
dim: 20330 1211 
metadata(3): Query: TCGAprepareParameters
  FilesInfo:
assays(2): raw_counts scaled_estimate
rownames(20330): A1BG|1 A1CF|29974 ...
  ZZEF1|23140 ZZZ3|26009
rowRanges metadata column names(3): gene_id
  entrezgene
  transcript_id.transcript_id_TCGA-E9-A1RD-11A-33R-A157-07
colnames(1211): TCGA-E9-A1RD-11A-33R-A157-07
  TCGA-E9-A1RC-01A-11R-A157-07 ...
  TCGA-D8-A1J9-01A-11R-A13Q-07
  TCGA-AC-A6IX-01A-12R-A32P-07
colData names(10): sample patient ... Siglust
  PAM50

> dataPrep <- TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)
Error in `colnames<-`(`*tmp*`, value = c("TCGA-E9-A1RD-11A-33R-A157-07",  : 
  length of 'dimnames' [2] not equal to array extent
  
  > sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] SummarizedExperiment_1.0.2 Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3         IRanges_2.4.6             
[6] S4Vectors_0.8.11           BiocGenerics_0.16.1        TCGAbiolinks_1.0.5        

loaded via a namespace (and not attached):
  [1] nlme_3.1-122                            bitops_1.0-6                            matrixStats_0.50.1                     
  [4] devtools_1.10.0                         doParallel_1.0.10                       RColorBrewer_1.1-2                     
  [7] httr_1.1.0                              Rgraphviz_2.14.0                        tools_3.2.3                            
 [10] R6_2.1.2                                affyio_1.40.0                           KernSmooth_2.23-15                     
 [13] DBI_0.3.1                               colorspace_1.2-6                        GGally_1.0.1                           
 [16] preprocessCore_1.32.0                   chron_2.3-47                            graph_1.48.0                           
 [19] rvest_0.3.1                             xml2_0.1.2                              sandwich_2.3-4                         
 [22] rtracklayer_1.30.1                      caTools_1.17.1                          scales_0.3.0                           
 [25] hexbin_1.27.1                           mvtnorm_1.0-5                           genefilter_1.52.1                      
 [28] affy_1.48.0                             DESeq_1.22.1                            stringr_1.0.0                          
 [31] supraHex_1.8.0                          digest_0.6.9                            Rsamtools_1.22.0                       
 [34] R.utils_2.2.0                           XVector_0.10.0                          limma_3.26.7                           
 [37] RSQLite_1.0.0                           BiocInstaller_1.20.1                    TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [40] zoo_1.7-12                              hwriter_1.3.2                           BiocParallel_1.4.3                     
 [43] gtools_3.5.0                            xlsx_0.5.7                              dplyr_0.4.3                            
 [46] R.oo_1.19.0                             RCurl_1.95-4.7                          magrittr_1.5                           
 [49] modeltools_0.2-21                       heatmap.plus_1.3                        futile.logger_1.4.1                    
 [52] Matrix_1.2-3                            Rcpp_0.12.3                             munsell_0.4.2                          
 [55] ape_3.4                                 R.methodsS3_1.7.0                       stringi_1.0-1                          
 [58] multcomp_1.4-3                          edgeR_3.12.0                            MASS_7.3-45                            
 [61] zlibbioc_1.16.0                         gplots_2.17.0                           plyr_1.8.3                             
 [64] grid_3.2.3                              gdata_2.17.0                            lattice_0.20-33                        
 [67] Biostrings_2.38.3                       splines_3.2.3                           xlsxjars_0.6.1                         
 [70] GenomicFeatures_1.22.12                 annotate_1.48.0                         EDASeq_2.4.1                           
 [73] igraph_1.0.1                            rjson_0.2.15                            geneplotter_1.48.0                     
 [76] codetools_0.2-14                        biomaRt_2.26.1                          futile.options_1.0.0                   
 [79] XML_3.98-1.3                            ShortRead_1.28.0                        downloader_0.4                         
 [82] latticeExtra_0.6-26                     lambda.r_1.1.7                          data.table_1.9.6                       
 [85] foreach_1.4.3                           gtable_0.1.2                            reshape_0.8.5                          
 [88] assertthat_0.1                          ggplot2_2.0.0                           dnet_1.0.7                             
 [91] aroma.light_3.0.0                       coin_1.1-2                              xtable_1.8-0                           
 [94] ConsensusClusterPlus_1.24.0             survival_2.38-3                         rJava_0.9-8                            
 [97] iterators_1.0.8                         GenomicAlignments_1.6.3                 AnnotationDbi_1.32.3                   
[100] memoise_1.0.0                           cluster_2.0.3                           TH.data_1.0-7   
  
ADD COMMENTlink modified 22 months ago • written 22 months ago by zeeniajagga0
1

One possibility is that one of the many packages you have loaded define a generic colnames<- or dimnames<- that interferes with the version of these functions TCGAbiolinks is expecting. Immediately after the error occurs, run the command traceback()

> dataPrep <- TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)
Error in `colnames<-`(`*tmp*`, value = c("TCGA-E9-A1RD-11A-33R-A157-07",  : 
  length of 'dimnames' [2] not equal to array extent
> traceback()
## WHAT IS YOUR OUTPUT HERE?

Also, it would be helpful to see the output of

> selectMethod("colnames<-", c(class(dataAssy), "character"))
## expect: Error... no method found for signature...
> selectMethod("dimnames<-", c(class(dataAssy), "list"))
## expect: a method definition from the SummarizedExperiment package
ADD REPLYlink written 22 months ago by Martin Morgan ♦♦ 21k

Ok, I ran in windows and I still have no problem. But I don't have these warnings below. Maybe some files were corrupted during download. Please, could you send me your dataAssy object?

 

1: In fread(files[i], header = TRUE, sep = "\t", stringsAsFactors = FALSE) :
  Stopped reading at empty line 14607 but text exists afterwards (discarded): RALA|589
2: In data.table::data.table(...) :
  Item 2 is of size 14605 but maximum size is 20531 (recycled leaving remainder of 5926 items)
3: In fread(files[i], header = TRUE, sep = "\t", stringsAsFactors = FALSE) :
  Stopped reading at empty line 2346 but text exists afterwards (discarded): C21orf57|54059    500.0
4: In data.table::data.table(...) :
  Item 2 is of size 2344 but maximum size is 20531 (recycled leaving remainder of 1779 items)

ADD REPLYlink written 22 months ago by tiagochst100

Here is the link to dataAssay object which has been created on my system

https://drive.google.com/file/d/0B9SRy5XoOWiENlU4UmNTMVBYRjA/view?usp=sharing

ADD REPLYlink written 22 months ago by zeeniajagga0

Your object is equal to mine except for two samples. I believe somehow some files were corrupted during download. And the package does not check for the data integrity. 

> assay(dataAssy)[15000:15002,492]
 SCO1|6341  SCO2|9997 SCOC|60592 
      5.00    4015.42    3398.00 
> assay(dataAssy2)[15000:15002,492]
 SCO1|6341  SCO2|9997 SCOC|60592 
      1731        644       9153 

The two files are unc.edu.6130b450-8b88-4a9a-b462-a34ec94183c9.1163157.rsem.genes.results and unc.edu.97b5ef6f-d621-4093-ab77-d60dcf706173.1152807.rsem.genes.results. 

Could you remove them from dataBRCA and run TCGADownload and TCGAPrepare again?

 

Also my object is here

You can run this command to see if the prepared data are equal

all(assay(dataAssy) == assay(dataAssy2))

Also TCGAanalyze_Preprocessing had a bug. The fix should be in bioconductor tonight (version 1.0.7). It is available in the github repository.

ADD REPLYlink written 22 months ago by tiagochst100

Your object is equal to mine except for two samples. I believe somehow some files were corrupted during download. And the package does not check for the data integrity. 

> assay(dataAssy)[15000:15002,492]
 SCO1|6341  SCO2|9997 SCOC|60592 
      5.00    4015.42    3398.00 
> assay(dataAssy2)[15000:15002,492]
 SCO1|6341  SCO2|9997 SCOC|60592 
      1731        644       9153 

The two files are unc.edu.6130b450-8b88-4a9a-b462-a34ec94183c9.1163157.rsem.genes.results and unc.edu.97b5ef6f-d621-4093-ab77-d60dcf706173.1152807.rsem.genes.results. 

Could you remove them from dataBRCA and run TCGADownload and TCGAPrepare again?

 

Also my object is here 

You can run this command to see if the prepared data are equal

all(assay(dataAssy) == assay(dataAssy2))

Also TCGAanalyze_Preprocessing had a bug. The fix should be in bioconductor tonight (version 1.0.7). It is available in the github repository.

ADD REPLYlink modified 22 months ago • written 22 months ago by tiagochst100

We just added the code to check data integrety, it is still in test. But could you reinstall and run your code again? 

The corrupted files should be redownloaded and TCGAPrepare should not show more warnings,

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
library(TCGAbiolinks)
ADD REPLYlink written 22 months ago by tiagochst100

@tiagochst Thank You  for looking into this error, I installed the new version of TCGA which is 1.0.7 and tried running through case 1. I am no more getting the Error in 'colnames'  issue, but now the error is at data filtering and data DEGs step..

here is complete run code including trace back and session info as well as comparison of the datAssay object

> library(SummarizedExperiment)
> library(TCGAbiolinks)
>
> cancer <- "BRCA"
> PlatformCancer <- "IlluminaHiSeq_RNASeqV2"
> dataType <- "rsem.genes.results"
> pathCancer <- paste0("../data",cancer)
>
> datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3")
> lsSample <- TCGAquery_samplesfilter(query = datQuery)
>
> # get subtype information
> dataSubt <- TCGAquery_subtype(tumor = cancer)
>
> # Which samples are Primary Solid Tumor
> dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample = "TP")
>
> # Which samples are Solid Tissue Normal
> dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample ="NT")
>
> # get clinical data
> dataClin <- TCGAquery_clinic(tumor = cancer, clinical_data_type = "clinical_patient")
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:1 files
| Path:./nationwidechildrens.org_BRCA.bio.Level_2.0.43.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |====================================================================================================================| 100%
Tumor type: BRCA
  |                                                                                                                    |   0%
Adding disease collumn to data frame
>
> TCGAdownload(data = datQuery,
+              path = pathCancer,
+              type = dataType,
+              samples = c(dataSmTP,dataSmTN))
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:1211 files
| Path:../dataBRCA/unc.edu_BRCA.IlluminaHiSeq_RNASeqV2.Level_3.1.11.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |====================================================================================================================| 100%
>
> dataAssy <- TCGAprepare(query = datQuery,
+                         dir = pathCancer,
+                         type = dataType,
+                         save = TRUE,
+                         summarizedExperiment = TRUE,
+                         samples = c(dataSmTP,dataSmTN),
+                         filename = paste0(cancer,"_",PlatformCancer,".rda"))
  |====================================================================================================================| 100%
Adding batch info to summarizedExperiment object

Adding metadata to the rse object...
Saving the data...
Data saved in: BRCA_IlluminaHiSeq_RNASeqV2.rda
Warning messages:
1: In fread(files[i], header = TRUE, sep = "\t", stringsAsFactors = FALSE) :
  Stopped reading at empty line 14607 but text exists afterwards (discarded): RALA|589
2: In data.table::data.table(...) :
  Item 2 is of size 14605 but maximum size is 20531 (recycled leaving remainder of 5926 items)
3: In fread(files[i], header = TRUE, sep = "\t", stringsAsFactors = FALSE) :
  Stopped reading at empty line 2346 but text exists afterwards (discarded): C21orf57|54059    500.0
4: In data.table::data.table(...) :
  Item 2 is of size 2344 but maximum size is 20531 (recycled leaving remainder of 1779 items)
>
> dataPrep <- TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)
> dataNorm <- TCGAanalyze_Normalization(tabDF = dataPrep, geneInfo = geneInfo, method = "gcContent")
[1] "I Need about  307 seconds for this Complete Normalization Upper Quantile  [Processing 80k elements /s]  "
[1] "Step 1 of 4: newSeqExpressionSet ..."
[1] "Step 2 of 4: withinLaneNormalization ..."
[1] "Step 3 of 4: betweenLaneNormalization ..."
[1] "Step 4 of 4: .quantileNormalization ..."
Warning message:
In geneNames[, 1] == names(tmp[which(tmp > 1)]) :
  longer object length is not a multiple of shorter object length
> dataFilt <- TCGAanalyze_Filtering(tabDF = dataNorm, method = "quantile", qnt.cut =  0.25)
> dataDEGs <- TCGAanalyze_DEA(mat1 = dataFilt[,dataSmTN], mat2 = dataFilt[,dataSmTP], Cond1type = "Normal",
+                            Cond2type = "Tumor", fdr.cut = 0.01 , logFC.cut = 1, method = "glmLRT")
Error in dataFilt[, dataSmTN] : subscript out of bounds

>  traceback()
2: cbind(mat1, mat2)
1: TCGAanalyze_DEA(mat1 = dataFilt[, dataSmTN], mat2 = dataFilt[,
       dataSmTP], Cond1type = "Normal", Cond2type = "Tumor", fdr.cut = 0.01,
       logFC.cut = 1, method = "glmLRT")
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] TCGAbiolinks_1.0.7         SummarizedExperiment_1.0.2 Biobase_2.30.0           
[4] GenomicRanges_1.22.4       GenomeInfoDb_1.6.3         IRanges_2.4.6            
[7] S4Vectors_0.8.11           BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
  [1] nlme_3.1-122                            bitops_1.0-6                          
  [3] matrixStats_0.50.1                      devtools_1.10.0                       
  [5] doParallel_1.0.10                       RColorBrewer_1.1-2                    
  [7] httr_1.1.0                              Rgraphviz_2.14.0                      
  [9] tools_3.2.3                             R6_2.1.2                              
[11] affyio_1.40.0                           KernSmooth_2.23-15                    
[13] DBI_0.3.1                               colorspace_1.2-6                      
[15] GGally_1.0.1                            preprocessCore_1.32.0                 
[17] chron_2.3-47                            graph_1.48.0                          
[19] rvest_0.3.1                             xml2_0.1.2                            
[21] sandwich_2.3-4                          rtracklayer_1.30.2                    
[23] caTools_1.17.1                          scales_0.3.0                          
[25] hexbin_1.27.1                           mvtnorm_1.0-5                         
[27] genefilter_1.52.1                       affy_1.48.0                           
[29] DESeq_1.22.1                            stringr_1.0.0                         
[31] supraHex_1.8.0                          digest_0.6.9                          
[33] Rsamtools_1.22.0                        R.utils_2.2.0                         
[35] XVector_0.10.0                          limma_3.26.8                          
[37] RSQLite_1.0.0                           BiocInstaller_1.20.1                  
[39] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 zoo_1.7-12                            
[41] hwriter_1.3.2                           BiocParallel_1.4.3                    
[43] gtools_3.5.0                            xlsx_0.5.7                            
[45] dplyr_0.4.3                             R.oo_1.19.0                           
[47] RCurl_1.95-4.7                          magrittr_1.5                          
[49] modeltools_0.2-21                       heatmap.plus_1.3                      
[51] futile.logger_1.4.1                     Matrix_1.2-3                          
[53] Rcpp_0.12.3                             munsell_0.4.3                         
[55] ape_3.4                                 R.methodsS3_1.7.0                     
[57] stringi_1.0-1                           multcomp_1.4-3                        
[59] edgeR_3.12.0                            MASS_7.3-45                           
[61] zlibbioc_1.16.0                         gplots_2.17.0                         
[63] plyr_1.8.3                              grid_3.2.3                            
[65] gdata_2.17.0                            lattice_0.20-33                       
[67] Biostrings_2.38.4                       splines_3.2.3                         
[69] xlsxjars_0.6.1                          GenomicFeatures_1.22.13               
[71] annotate_1.48.0                         EDASeq_2.4.1                          
[73] igraph_1.0.1                            rjson_0.2.15                          
[75] geneplotter_1.48.0                      codetools_0.2-14                      
[77] biomaRt_2.26.1                          futile.options_1.0.0                  
[79] XML_3.98-1.3                            ShortRead_1.28.0                      
[81] downloader_0.4                          latticeExtra_0.6-28                   
[83] lambda.r_1.1.7                          data.table_1.9.6                      
[85] foreach_1.4.3                           gtable_0.1.2                          
[87] reshape_0.8.5                           assertthat_0.1                        
[89] ggplot2_2.0.0                           dnet_1.0.7                            
[91] aroma.light_3.0.0                       coin_1.1-2                            
[93] xtable_1.8-2                            ConsensusClusterPlus_1.24.0           
[95] survival_2.38-3                         rJava_0.9-8                           
[97] iterators_1.0.8                         GenomicAlignments_1.6.3               
[99] AnnotationDbi_1.32.3                    memoise_1.0.0                         
[101] cluster_2.0.3                           TH.data_1.0-7   

 

And upon comparing the datAssay object of yours and the one generate on my system ( can be accessed @ https://drive.google.com/open?id=0B9SRy5XoOWiEbllNalIxaTZSVk0), its not same and differs as following

> load(file = "C://.../TCGA_biolinks/dataAssy2.rda")
> all(assay(dataAssy) == assay(dataAssy2))
[1] FALSE
> all.equal(dataAssy,dataAssy2)
[1] "Attributes: < Component “assays”: Class definitions are not identical >"                                                        
[2] "Attributes: < Component “metadata”: Component “Query:”: Component 1: Attributes: < Component “row.names”: 1 string mismatch > >"
[3] "Attributes: < Component “metadata”: Component “FilesInfo:”: Component 1: Component 1: Mean absolute difference: 637854.9 >"     
[4] "Attributes: < Component “metadata”: Component “FilesInfo:”: Component 1: Component 2: Mean absolute difference: 637868.1 >"  

 

 

ADD REPLYlink modified 22 months ago • written 22 months ago by zeeniajagga0

As there were outliers, the data frame lost some columns. But 

 dataFilt[, dataSmTN]

is considering the object has them all. The code should be something like?

dataDEGs <- TCGAanalyze_DEA(mat1 = subset(dataFilt, select = colnames(dataFilt) %in% dataSmTN),
                            mat2 = subset(dataFilt, select = colnames(dataFilt) %in% dataSmTP),
                            Cond1type = "Normal",
                            Cond2type = "Tumor",
                            fdr.cut = 0.01 ,
                            logFC.cut = 1,
                            method = "glmLRT")  

 

About the data download, I saw you are using 1.0.7, it does not have the verification of downloaded files. So it is not going to correct the files. Please install it with:

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

and rerun the code.

 

ADD REPLYlink written 22 months ago by tiagochst100

I am not able to install from devtools. Am I doing something wrong??

> devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master
Installing TCGAbiolinks
Skipping 2 unavailable packages: ALL, TxDb.Hsapiens.UCSC.hg19.knownGene
Installing 1 package: IRanges
Warning: package ‘IRanges’ is in use and will not be installed
"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/bioxcel/AppData/Local/Temp/RtmpU9iTrz/devtools95c66b342ad/BioinformaticsFMRP-TCGAbiolinks-3b6b954"  \
  --library="C:/Users/bioxcel/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'nlme' 3.1-122 is being loaded, but >= 3.1.123 is required
ERROR: lazy loading failed for package 'TCGAbiolinks'
* removing 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks'
* restoring previous 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks'
Error: Command failed (1)
ADD REPLYlink modified 22 months ago • written 22 months ago by zeeniajagga0

nlme is outdated. Try updating the packages or installing the last version manually https://cran.r-project.org/web/packages/nlme/index.html (the last version is 3.1-124)

ADD REPLYlink written 22 months ago by tiagochst100

updated nlme; Now the installation process has come up with three more errors

> devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master
Installing TCGAbiolinks
Skipping 2 unavailable packages: ALL, TxDb.Hsapiens.UCSC.hg19.knownGene
Installing 1 package: IRanges
Warning: package ‘IRanges’ is in use and will not be installed
"C:/PROGRA~1/R/R-32~1.3/bin/x64/R"  \
  --no-site-file --no-environ --no-save  \
  --no-restore CMD INSTALL  \
 "C:/Users/bioxcel/AppData/Local/Temp/RtmpMvZk61/devtools15383f71431/BioinformaticsFMRP-TCGAbiolinks-3b6b954"  \
  --library="C:/Users/bioxcel/Documents/R/win-library/3.2"  \
  --install-tests 
* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: No CurrentVersion entry in Software/JavaSoft registry! Try re-installing Java and make sure R and Java have matching architectures.
Error: loading failed
Execution halted
*** arch - x64
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
ERROR: loading failed for 'i386'
* removing 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks'
* restoring previous 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks'
Error: Command failed (1)
> system("java -version")
java version "1.8.0_73"
Java(TM) SE Runtime Environment (build 1.8.0_73-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.73-b02, mixed mode)

> devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master
Installing TCGAbiolinks
Skipping 2 unavailable packages: ALL, TxDb.Hsapiens.UCSC.hg19.knownGene
Installing 1 package: IRanges
Warning: package ‘IRanges’ is in use and will not be installed
"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/bioxcel/AppData/Local/Temp/RtmpSIhHjc/devtools1b4c6e24419/BioinformaticsFMRP-TCGAbiolinks-3b6b954"  \
  --library="C:/Users/bioxcel/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: No CurrentVersion entry in Software/JavaSoft registry! Try re-installing Java and make sure R and Java have matching architectures.
Error: loading failed
Execution halted
*** arch - x64
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
ERROR: loading failed for 'i386'
* removing 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks'
* restoring previous 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks'
Error: Command failed (1)
> traceback()
10: stop("Command failed (", status, ")", call. = FALSE)
9: system_check(r_path, options, c(r_profile(), r_env_vars(), env_vars), 
       ...)
8: force(code)
7: withr::with_dir(path, system_check(r_path, options, c(r_profile(), 
       r_env_vars(), env_vars), ...))
6: R(paste("CMD INSTALL ", shQuote(built_path), " ", opts, sep = ""), 
       quiet = quiet)
5: install(source, ..., quiet = quiet, metadata = metadata)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = logical(1))
2: install_remotes(remotes, quiet = quiet, ...)
1: devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

 

Strangely, one of the complaint is for java, but java on my system is updated:

> system("java -version")
java version "1.8.0_73"
Java(TM) SE Runtime Environment (build 1.8.0_73-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.73-b02, mixed mode)

 

How to resolve this?

ADD REPLYlink written 22 months ago by zeeniajagga0
Your R is 32 bits: "C:/PROGRA~1/R/R-32~1.3/bin/x64/R" And your java is 64-Bit Probably you'll need to install or java 32 or are 64. They need to have matching architectures. Did you try some of these links? https://stackoverflow.com/questions/17376939/problems-when-trying-to-load-a-package-in-r-due-to-rjava https://cran.r-project.org/web/packages/gMCP/INSTALL Tiago Chedraoui Silva
ADD REPLYlink modified 22 months ago by Dan Tenenbaum ♦♦ 8.2k • written 22 months ago by tiagochst100

I am able to install TCGAbiolinks from git hub repo with few warnings and while downloading the corrupted file, it is entering into an infinite loop..

​> devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master
Installing TCGAbiolinks
Skipping 2 unavailable packages: ALL, TxDb.Hsapiens.UCSC.hg19.knownGene
Installing 1 package: IRanges
Warning: package ‘IRanges’ is in use and will not be installed
"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/bioxcel/AppData/Local/Temp/Rtmp0gncV8/devtools147cf45485a/BioinformaticsFMRP-TCGAbiolinks-3b6b954"  \
  --library="C:/Users/bioxcel/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* DONE (TCGAbiolinks)
> library(SummarizedExperiment)
> library(TCGAbiolinks)
>
> cancer <- "BRCA"
> PlatformCancer <- "IlluminaHiSeq_RNASeqV2"
> dataType <- "rsem.genes.results"
> pathCancer <- paste0("../data",cancer)
>
> datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3")
> lsSample <- TCGAquery_samplesfilter(query = datQuery)
>
> # get subtype information
> dataSubt <- TCGAquery_subtype(tumor = cancer)
>
> # Which samples are Primary Solid Tumor
> dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample = "TP")
>
> # Which samples are Solid Tissue Normal
> dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample ="NT")
>
> # get clinical data
> dataClin <- TCGAquery_clinic(tumor = cancer, clinical_data_type = "clinical_patient")
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100   765  100   765    0     0    590      0  0:00:01  0:00:01 --:--:--   598
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:1 files
| Path:./nationwidechildrens.org_BRCA.bio.Level_2.0.43.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |                                                                                                    |   0%
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt

This downloaded file might be corrupted, we are downloading it again.
[1] nationwidechildrens.org_clinical_patient_brca.txt
ADD REPLYlink written 22 months ago by zeeniajagga0
I'm sorry, this was an windows specifc bug. I believe I solved it. Please, could you reinstall it and try again devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") Tiago Chedraoui Silva On Wed, Feb 17, 2016 at 3:53 AM, zeeniajagga [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User zeeniajagga <https: support.bioconductor.org="" u="" 9678=""/> wrote Comment: > Error in 'colnames' while running case 1 of TCGABiolinks > <https: support.bioconductor.org="" p="" 77982="" #78431="">: > > I am able to install TCGAbiolinks from git hub repo with few warnings and > while downloading the corrupted file, it is entering into an infinite loop.. > > ​> devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") > Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master > from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master > Installing TCGAbiolinks > Skipping 2 unavailable packages: ALL, TxDb.Hsapiens.UCSC.hg19.knownGene > Installing 1 package: IRanges > Warning: package ‘IRanges’ is in use and will not be installed > "C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL \ > "C:/Users/bioxcel/AppData/Local/Temp/Rtmp0gncV8/devtools147cf45485a/BioinformaticsFMRP-TCGAbiolinks-3b6b954" \ > --library="C:/Users/bioxcel/Documents/R/win-library/3.2" --install-tests > > * installing *source* package 'TCGAbiolinks' ... > ** R > ** data > *** moving datasets to lazyload DB > ** inst > ** tests > ** preparing package for lazy loading > Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class. > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded > Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class. > * DONE (TCGAbiolinks) > > library(SummarizedExperiment) > > library(TCGAbiolinks) > > > > cancer <- "BRCA" > > PlatformCancer <- "IlluminaHiSeq_RNASeqV2" > > dataType <- "rsem.genes.results" > > pathCancer <- paste0("../data",cancer) > > > > datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3") > > lsSample <- TCGAquery_samplesfilter(query = datQuery) > > > > # get subtype information > > dataSubt <- TCGAquery_subtype(tumor = cancer) > > > > # Which samples are Primary Solid Tumor > > dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample = "TP") > > > > # Which samples are Solid Tissue Normal > > dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample ="NT") > > > > # get clinical data > > dataClin <- TCGAquery_clinic(tumor = cancer, clinical_data_type = "clinical_patient") > % Total % Received % Xferd Average Speed Time Time Time Current > Dload Upload Total Spent Left Speed > 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 765 100 765 0 0 590 0 0:00:01 0:00:01 --:--:-- 598 > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > | Downloading:1 files > | Path:./nationwidechildrens.org_BRCA.bio.Level_2.0.43.0 > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > | | 0% > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > This downloaded file might be corrupted, we are downloading it again. > [1] nationwidechildrens.org_clinical_patient_brca.txt > > ------------------------------ > > Post tags: tcgabiolinks, Error in `colnames > > You may reply via email or visit > C: Error in 'colnames' while running case 1 of TCGABiolinks >
ADD REPLYlink written 22 months ago by tiagochst100

Still not able to install from github on Windows R studio, here is the 

> devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master
Installing TCGAbiolinks
Skipping 2 unavailable packages: ALL, TxDb.Hsapiens.UCSC.hg19.knownGene
Installing 1 package: IRanges
Warning: package ‘IRanges’ is in use and will not be installed
"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/bioxcel/AppData/Local/Temp/Rtmp0gncV8/devtools147c13c166eb/BioinformaticsFMRP-TCGAbiolinks-c73bb0f"  \
  --library="C:/Users/bioxcel/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'TCGAbiolinks' ...
Warning in file.copy(f, instdir, TRUE) :
  problem copying .\NAMESPACE to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\NAMESPACE: Permission denied
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks/DESCRIPTION': No such file or directory
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'TCGAbiolinks'
* restoring previous 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\CITATION to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\CITATION: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem creating directory C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\data: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\DESCRIPTION to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\DESCRIPTION: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem creating directory C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\help: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem creating directory C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\html: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\INDEX to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\INDEX: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem creating directory C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\Meta: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\NAMESPACE to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\NAMESPACE: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem copying C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\NEWS to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\NEWS: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem creating directory C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\R: No such file or directory
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problem creating directory C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\tests: No such file or directory
Error: Command failed (1)

> traceback()
10: stop("Command failed (", status, ")", call. = FALSE)
9: system_check(r_path, options, c(r_profile(), r_env_vars(), env_vars), 
       ...)
8: force(code)
7: withr::with_dir(path, system_check(r_path, options, c(r_profile(), 
       r_env_vars(), env_vars), ...))
6: R(paste("CMD INSTALL ", shQuote(built_path), " ", opts, sep = ""), 
       quiet = quiet)
5: install(source, ..., quiet = quiet, metadata = metadata)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = logical(1))
2: install_remotes(remotes, quiet = quiet, ...)
1: devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

 

As you said this might be windows specific error, so I tried it with RStudio server, though I am able to install TCGAbiolinks but error while downloading the file, it seems to me that TCGA link for the BRCA RNASeq datasets has changed 

> library(SummarizedExperiment)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist, unsplit

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To
    cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

> library(TCGAbiolinks)
> 
> cancer <- "BRCA"
> PlatformCancer <- "IlluminaHiSeq_RNASeqV2"
> dataType <- "rsem.genes.results"
> pathCancer <- paste0("../data",cancer)
> 
> datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3")
> lsSample <- TCGAquery_samplesfilter(query = datQuery)
> 
> # get subtype information
> dataSubt <- TCGAquery_subtype(tumor = cancer)
> 
> # Which samples are Primary Solid Tumor
> dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample = "TP")
> 
> # Which samples are Solid Tissue Normal
> dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample ="NT")
> 
> # get clinical data
> dataClin <- TCGAquery_clinic(tumor = cancer, clinical_data_type = "clinical_patient")
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100   765  100   765    0     0   1016      0 --:--:-- --:--:-- --:--:--  1017
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:1 files
| Path:./nationwidechildrens.org_BRCA.bio.Level_2.0.43.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |                                                                                |   0%
[1] nationwidechildrens.org_clinical_patient_brca.txt

  |================================================================================| 100%
Tumor type: BRCA
  |                                                                                |   0%
Adding disease collumn to data frame
> 
> TCGAdownload(data = datQuery,
+              path = pathCancer,
+              type = dataType,
+              samples = c(dataSmTP,dataSmTN))
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 80970    0 80970    0     0  56407      0 --:--:--  0:00:01 --:--:-- 56385100  216k    0  216k    0     0   128k      0 --:--:--  0:00:01 --:--:--  128k
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
| Downloading:1211 files
| Path:../dataBRCA/unc.edu_BRCA.IlluminaHiSeq_RNASeqV2.Level_3.1.11.0
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
  |                                                                                |   0%
[1] unc.edu.000d877f-8d03-44bc-8607-27b5ba84b5fe.1167702.rsem.genes.results

Error in download.file(url, method = method, ...) : 
  cannot open destfile '../dataBRCA/unc.edu_BRCA.IlluminaHiSeq_RNASeqV2.Level_3.1.11.0/unc.edu.000d877f-8d03-44bc-8607-27b5ba84b5fe.1167702.rsem.genes.results', reason 'No such file or directory'
> 

 

ADD REPLYlink written 22 months ago by zeeniajagga0
Could you see if this is the same error: http://stackoverflow.com/questions/32420581/error-installing-r-package-code-tools Permission denied is saying you don't have permission do erase the files. And 00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks says there is a lock. So either the lock is still there and you need to remove it or you need to be sudo (run R as administrator) to have the permission. Tiago Chedraoui Silva On Thu, Feb 18, 2016 at 4:34 AM, zeeniajagga [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User zeeniajagga <https: support.bioconductor.org="" u="" 9678=""/> wrote Comment: > Error in 'colnames' while running case 1 of TCGABiolinks > <https: support.bioconductor.org="" p="" 77982="" #78498="">: > > Still not able to install from github on Windows R studio, here is the > ​ > > devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") > Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master > from URL > https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master > Installing TCGAbiolinks > Skipping 2 unavailable packages: ALL, TxDb.Hsapiens.UCSC.hg19.knownGene > Installing 1 package: IRanges > Warning: package ‘IRanges’ is in use and will not be installed > "C:/PROGRA~1/R/R-32~1.3/bin/x64/R" --no-site-file --no-environ --no-save > --no-restore CMD INSTALL \ > > "C:/Users/bioxcel/AppData/Local/Temp/Rtmp0gncV8/devtools147c13c166eb/BioinformaticsFMRP-TCGAbiolinks-c73bb0f" > \ > --library="C:/Users/bioxcel/Documents/R/win-library/3.2" --install-tests > > * installing *source* package 'TCGAbiolinks' ... > Warning in file.copy(f, instdir, TRUE) : > problem copying .\NAMESPACE to > C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\NAMESPACE: > Permission denied > Warning in file(file, ifelse(append, "a", "w")) : > cannot open file > 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks/DESCRIPTION': No > such file or directory > Error in file(file, ifelse(append, "a", "w")) : > cannot open the connection > ERROR: installing package DESCRIPTION failed for package 'TCGAbiolinks' > * restoring previous > 'C:/Users/bioxcel/Documents/R/win-library/3.2/TCGAbiolinks' > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem copying > C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\CITATION > to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\CITATION: No > such file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem creating directory > C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\data: No such > file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem copying > C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\DESCRIPTION > to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\DESCRIPTION: > No such file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem creating directory > C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\help: No such > file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem creating directory > C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\html: No such > file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem copying > C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\INDEX > to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\INDEX: No such > file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem creating directory > C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\Meta: No such > file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem copying > C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\NAMESPACE > to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\NAMESPACE: No > such file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem copying > C:\Users\bioxcel\Documents\R\win-library\3.2\00LOCK-BioinformaticsFMRP-TCGAbiolinks-c73bb0f\TCGAbiolinks\NEWS > to C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\NEWS: No such > file or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem creating directory > C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\R: No such file > or directory > Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = > TRUE) : > problem creating directory > C:\Users\bioxcel\Documents\R\win-library\3.2\TCGAbiolinks\tests: No such > file or directory > Error: Command failed (1) > > > traceback() > 10: stop("Command failed (", status, ")", call. = FALSE) > 9: system_check(r_path, options, c(r_profile(), r_env_vars(), env_vars), > ...) > 8: force(code) > 7: withr::with_dir(path, system_check(r_path, options, c(r_profile(), > r_env_vars(), env_vars), ...)) > 6: R(paste("CMD INSTALL ", shQuote(built_path), " ", opts, sep = ""), > quiet = quiet) > 5: install(source, ..., quiet = quiet, metadata = metadata) > 4: FUN(X[[i]], ...) > 3: vapply(remotes, install_remote, ..., FUN.VALUE = logical(1)) > 2: install_remotes(remotes, quiet = quiet, ...) > 1: devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") > > > > As you said this might be windows specific error, so I tried it with > RStudio server, though I am able to install TCGAbiolinks but error while > downloading the file, it seems to me that TCGA link for the BRCA RNASeq > datasets has changed > > > library(SummarizedExperiment) > Loading required package: GenomicRanges > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ‘BiocGenerics’ > > The following objects are masked from ‘package:parallel’: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, > clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, > parSapply, parSapplyLB > > The following objects are masked from ‘package:stats’: > > IQR, mad, xtabs > > The following objects are masked from ‘package:base’: > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, > duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, > is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, > pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, > setdiff, sort, table, tapply, union, unique, unlist, unsplit > > Loading required package: S4Vectors > Loading required package: stats4 > Loading required package: IRanges > Loading required package: GenomeInfoDb > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with 'browseVignettes()'. To > cite Bioconductor, see 'citation("Biobase")', and for packages > 'citation("pkgname")'. > > > library(TCGAbiolinks) > > > > cancer <- "BRCA" > > PlatformCancer <- "IlluminaHiSeq_RNASeqV2" > > dataType <- "rsem.genes.results" > > pathCancer <- paste0("../data",cancer) > > > > datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3") > > lsSample <- TCGAquery_samplesfilter(query = datQuery) > > > > # get subtype information > > dataSubt <- TCGAquery_subtype(tumor = cancer) > > > > # Which samples are Primary Solid Tumor > > dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample = "TP") > > > > # Which samples are Solid Tissue Normal > > dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2, typesample ="NT") > > > > # get clinical data > > dataClin <- TCGAquery_clinic(tumor = cancer, clinical_data_type = "clinical_patient") > % Total % Received % Xferd Average Speed Time Time Time Current > Dload Upload Total Spent Left Speed > 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 765 100 765 0 0 1016 0 --:--:-- --:--:-- --:--:-- 1017 > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > | Downloading:1 files > | Path:./nationwidechildrens.org_BRCA.bio.Level_2.0.43.0 > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > | | 0% > [1] nationwidechildrens.org_clinical_patient_brca.txt > > |================================================================================| 100% > Tumor type: BRCA > | | 0% > Adding disease collumn to data frame > > > > TCGAdownload(data = datQuery, > + path = pathCancer, > + type = dataType, > + samples = c(dataSmTP,dataSmTN)) > % Total % Received % Xferd Average Speed Time Time Time Current > Dload Upload Total Spent Left Speed > 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 80970 0 80970 0 0 56407 0 --:--:-- 0:00:01 --:--:-- 56385100 216k 0 216k 0 0 128k 0 --:--:-- 0:00:01 --:--:-- 128k > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > | Downloading:1211 files > | Path:../dataBRCA/unc.edu_BRCA.IlluminaHiSeq_RNASeqV2.Level_3.1.11.0 > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > | | 0% > [1] unc.edu.000d877f-8d03-44bc-8607-27b5ba84b5fe.1167702.rsem.genes.results > > Error in download.file(url, method = method, ...) : > cannot open destfile '../dataBRCA/unc.edu_BRCA.IlluminaHiSeq_RNASeqV2.Level_3.1.11.0/unc.edu.000d877f-8d03-44bc-8607-27b5ba84b5fe.1167702.rsem.genes.results', reason 'No such file or directory' > > > > > > ------------------------------ > > Post tags: tcgabiolinks, Error in `colnames > > You may reply via email or visit > C: Error in 'colnames' while running case 1 of TCGABiolinks >
ADD REPLYlink written 22 months ago by tiagochst100

I see this error. If I

options(error=recover)

and then run

dataPrep <- TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)

I get to

Enter a frame number, or 0 to exit   

1: TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)
2: `colnames<-`(`*tmp*`, value = c("TCGA-E9-A1RD-11A-33R-A157-07", "TCGA-E9-A1

Selection: 

Entering '1' and exploring a bit, I seem I'm at the last several lines of the function

    samplesCor <- rowMeans(c)
    objectWO <-  assay(object,"raw_counts")[, samplesCor > cor.cut]
    colnames(objectWO) <- colData(object)$sample

and that the subset leading to objectW0 drops one column

Browse[1]> table(samplesCor > cor.cut)

FALSE  TRUE 
    1  1210 

so the attempt to update the colnames() has the wrong length; it should be

colnames(objectWO) <- colData(object)$sample[samplesCor > cor.cut]

I'm not sure why the example is not reproducible by @tiagochst; maybe the upstream files have changed, and the attempt to reproduce uses a cache?

I was impressed with the clear design of the package, especially that my download recovered rather than starting over!

> R.version[c("platform", "version.string")]
               _                                          
platform       x86_64-pc-linux-gnu                        
version.string R version 3.2.3 Patched (2016-01-28 r70038)

 

ADD REPLYlink modified 22 months ago • written 22 months ago by Martin Morgan ♦♦ 21k

Yes, it's a bug. Using a cor.cut higher I could reproduce the error, but why it is not reproducible with the same cor.cut was quite strange. 

ADD REPLYlink written 22 months ago by tiagochst100
0
gravatar for zeeniajagga
22 months ago by
zeeniajagga0 wrote:

Below is the output for traceback as well as selectMethod; and the output for select method matches the expected output

​> dataPrep <- TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)
Error in `colnames<-`(`*tmp*`, value = c("TCGA-E9-A1RD-11A-33R-A157-07",  :
  length of 'dimnames' [2] not equal to array extent

> traceback()
2: `colnames<-`(`*tmp*`, value = c("TCGA-E9-A1RD-11A-33R-A157-07",
   "TCGA-E9-A1RC-01A-11R-A157-07", "TCGA-AC-A8OP-01A-11R-A36F-07",
...
   "TCGA-D8-A1J9-01A-11R-A13Q-07", "TCGA-AC-A6IX-01A-12R-A32P-07"
   ))
1: TCGAanalyze_Preprocessing(object = dataAssy, cor.cut = 0.6)

> selectMethod("colnames<-", c(class(dataAssy), "character"))
Error in selectMethod("colnames<-", c(class(dataAssy), "character")) :
  no method found for signature RangedSummarizedExperiment, character
> selectMethod("dimnames<-", c(class(dataAssy), "list"))
Method Definition:

function (x, value)
{
    rowRanges <- rowRanges(x)
    names(rowRanges) <- value[[1]]
    colData <- colData(x)
    rownames(colData) <- value[[2]]
    BiocGenerics:::replaceSlots(x, rowRanges = rowRanges, colData = colData,
        check = FALSE)
}
<environment: namespace:SummarizedExperiment>

Signatures:
        x                            value
target  "RangedSummarizedExperiment" "list"
defined "RangedSummarizedExperiment" "list" 
ADD COMMENTlink modified 22 months ago by Martin Morgan ♦♦ 21k • written 22 months ago by zeeniajagga0
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