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meganlloyd
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@meganlloyd-22531
Last seen 4.9 years ago
Hi everyone,
I'd very much appreciate any help/advice you can offer. I am trying to analyse publically available 3' microarray data - available here https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6969/?array=A-MTAB-599
- I have an array annotation txt file but no cdf file. When I run this code:
**library(affy)
library(limma)
library(Biobase)
celpath = "C:/Users/hp/Documents/Research/DDIR/raw data/DDIR CEL"
data = ReadAffy(celfile.path=celpath)
data**
- I get:
>AffyBatch object
>size of arrays=1164x1164 features (130 kb)
>cdf=ADXECv1a520743 (??? affyids)
>number of samples=273
>Error in getCdfInfo(object) :
>Could not obtain CDF environment, problems encountered:
>Specified environment does not contain ADXECv1a520743
>Library - package adxecv1a520743cdf not installed
>Bioconductor - adxecv1a520743cdf not available
>In addition: Warning message:
>missing cdf environment! in show(AffyBatch)
- I tried to install the package:
**BiocManager::install("adxecv1a520743cdf")**
- But got this error:
> package ‘adxecv1a520743cdf’ is not available (for R version 3.6.1)
I'm at a bit of a loss as to what to try next. Any help would be very much appreciated! Thank you :)
This is my session info
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] pdInfoBuilder_1.48.0 affxparser_1.56.0 RSQLite_2.1.2
[4] oligo_1.48.0 oligoClasses_1.46.0 makecdfenv_1.60.0
[7] affyio_1.54.0 genefilter_1.66.0 Biostrings_2.52.0
[10] XVector_0.24.0 survminer_0.4.6 ggpubr_0.2.3
[13] magrittr_1.5 survival_2.44-1.1 gridExtra_2.3
[16] glmnet_2.0-18 foreach_1.4.7 Matrix_1.2-17
[19] MASS_7.3-51.4 pheatmap_1.0.12 EnhancedVolcano_1.2.0
[22] ggrepel_0.8.1 DESeq2_1.24.0 SummarizedExperiment_1.14.1
[25] DelayedArray_0.10.0 BiocParallel_1.18.1 matrixStats_0.55.0
[28] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 reshape_0.8.8
[31] RColorBrewer_1.1-2 org.Mm.eg.db_3.8.2 AnnotationDbi_1.46.1
[34] IRanges_2.18.3 S4Vectors_0.22.1 Biobase_2.44.0
[37] BiocGenerics_0.30.0 gplots_3.0.1.1 Glimma_1.12.0
[40] edgeR_3.26.8 limma_3.40.6 readxl_1.3.1
[43] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3
[46] purrr_0.3.2 readr_1.3.1 tidyr_1.0.0
[49] tibble_2.1.3 ggplot2_3.2.1 tidyverse_1.2.1
[52] NormExpression_0.1.0
loaded via a namespace (and not attached):
[1] backports_1.1.5 Hmisc_4.2-0 plyr_1.8.4
[4] lazyeval_0.2.2 splines_3.6.1 digest_0.6.21
[7] htmltools_0.4.0 gdata_2.18.0 checkmate_1.9.4
[10] memoise_1.1.0 cluster_2.1.0 annotate_1.62.0
[13] modelr_0.1.5 colorspace_1.4-1 blob_1.2.0
[16] rvest_0.3.5 haven_2.1.1 xfun_0.11
[19] crayon_1.3.4 RCurl_1.95-4.12 jsonlite_1.6
[22] zeallot_0.1.0 zoo_1.8-6 iterators_1.0.12
[25] glue_1.3.1 gtable_0.3.0 zlibbioc_1.30.0
[28] scales_1.0.0 DBI_1.0.0 Rcpp_1.0.2
[31] xtable_1.8-4 htmlTable_1.13.3 foreign_0.8-71
[34] bit_1.1-14 preprocessCore_1.46.0 km.ci_0.5-2
[37] Formula_1.2-3 htmlwidgets_1.5.1 httr_1.4.1
[40] acepack_1.4.1 ff_2.2-14 pkgconfig_2.0.3
[43] XML_3.98-1.20 nnet_7.3-12 locfit_1.5-9.1
[46] tidyselect_0.2.5 labeling_0.3 rlang_0.4.0
[49] munsell_0.5.0 cellranger_1.1.0 tools_3.6.1
[52] cli_2.0.0 generics_0.0.2 broom_0.5.2
[55] knitr_1.26 bit64_0.9-7 survMisc_0.5.5
[58] caTools_1.17.1.2 nlme_3.1-140 xml2_1.2.2
[61] compiler_3.6.1 rstudioapi_0.10 ggsignif_0.6.0
[64] geneplotter_1.62.0 stringi_1.4.3 lattice_0.20-38
[67] KMsurv_0.1-5 vctrs_0.2.0 pillar_1.4.2
[70] lifecycle_0.1.0 BiocManager_1.30.10 data.table_1.12.4
[73] bitops_1.0-6 R6_2.4.1 latticeExtra_0.6-28
[76] affy_1.62.0 KernSmooth_2.23-15 codetools_0.2-16
[79] gtools_3.8.1 assertthat_0.2.1 withr_2.1.2
[82] GenomeInfoDbData_1.2.1 hms_0.5.2 rpart_4.1-15
[85] lubridate_1.7.4 base64enc_0.1-3
Thank you so much!! Works a treat :D