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kasperdanielhansen / genbioconductor

Materials for Genomics Data Science: Introduction to Bioconductor
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no such column: man_fsetid #5

Closed Elkoumy closed 8 years ago

Elkoumy commented 8 years ago

Dear Sir, When I run the command rma(rawData) I got the following error: Error in sqliteSendQuery(con, statement, bind.data) : error in statement: no such column: man_fsetid

My cell file from ebi.ac.uk Please support.

kasperdanielhansen commented 8 years ago

1) is you version fully updated (run biocValid())? 2) what array are you using (just print the rawData file and see).

Kasper

On Thu, May 26, 2016 at 8:31 AM, Jamal notifications@github.com wrote:

Dear Sir, When I run the command rma(rawData) I got the following error: Error in sqliteSendQuery(con, statement, bind.data) : error in statement: no such column: man_fsetid

My cell file from ebi.ac.uk Please support.

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Elkoumy commented 8 years ago

rawData SnpCnvFeatureSet (storageMode: lockedEnvironment) assayData: 6892960 features, 2 samples element names: exprs protocolData rowNames: ega-box-04_MB-0402 ega-box-04_MB-0421 varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: ega-box-04_MB-0402 ega-box-04_MB-0421 varLabels: index filename varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.genomewidesnp.6

biocValid()

R version 3.3.0 (2016-05-03) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows >= 8 x64 (build 9200)

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] pd.genomewidesnp.6_3.14.1 RSQLite_1.0.0 DBI_0.4-1
[4] oligo_1.36.1 Biostrings_2.40.1 XVector_0.12.0
[7] IRanges_2.6.0 S4Vectors_0.10.1 oligoClasses_1.34.0
[10] BiocInstaller_1.22.2 Biobase_2.32.0 BiocGenerics_0.18.0

loaded via a namespace (and not attached): [1] affxparser_1.44.0 splines_3.3.0 GenomicRanges_1.24.0
[4] zlibbioc_1.18.0 bit_1.1-12 foreach_1.4.3
[7] GenomeInfoDb_1.8.2 tools_3.3.0 SummarizedExperiment_1.2.2 [10] ff_2.2-13 iterators_1.0.8 preprocessCore_1.34.0
[13] affyio_1.42.0 codetools_0.2-14

downgrade with biocLite("GenomeInfoDb")

Error: 1 package(s) too new

kasperdanielhansen commented 8 years ago

This is a genotyping array. RMA is a preprocessing function for expression arrays; you can't use it on Genotyping arrays.

Best, Kasper

On Thu, May 26, 2016 at 2:21 PM, Jamal notifications@github.com wrote:

rawData SnpCnvFeatureSet (storageMode: lockedEnvironment) assayData: 6892960 features, 2 samples element names: exprs protocolData rowNames: ega-box-04_MB-0402 ega-box-04_MB-0421 varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: ega-box-04_MB-0402 ega-box-04_MB-0421 varLabels: index filename varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)'

Annotation: pd.genomewidesnp.6

biocValid()

  • sessionInfo()

R version 3.3.0 (2016-05-03) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows >= 8 x64 (build 9200)

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

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

[9] base

other attached packages: [1] pd.genomewidesnp.6_3.14.1 RSQLite_1.0.0 DBI_0.4-1

[4] oligo_1.36.1 Biostrings_2.40.1 XVector_0.12.0

[7] IRanges_2.6.0 S4Vectors_0.10.1 oligoClasses_1.34.0

[10] BiocInstaller_1.22.2 Biobase_2.32.0 BiocGenerics_0.18.0

loaded via a namespace (and not attached): [1] affxparser_1.44.0 splines_3.3.0 GenomicRanges_1.24.0

[4] zlibbioc_1.18.0 bit_1.1-12 foreach_1.4.3

[7] GenomeInfoDb_1.8.2 tools_3.3.0 SummarizedExperiment_1.2.2 [10] ff_2.2-13 iterators_1.0.8 preprocessCore_1.34.0

[13] affyio_1.42.0 codetools_0.2-14

-

Packages too new for Bioconductor version '3.3'

    Version LibPath

GenomeInfoDb "1.8.2" "C:/Users/Gamal/Documents/R/win-library/3.3"

downgrade with biocLite("GenomeInfoDb")

Error: 1 package(s) too new

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Elkoumy commented 8 years ago

Thank you for your reply. Could you please tell me the best package to normalize the genotyping array? Regards, Jamal

kasperdanielhansen commented 8 years ago

What you want for genotyping arrays is usually either genotype calls or copy number calls or both. This is an area with lots of options. You could start by looking into the CRLMM package on Bioconductor.

Best, Kasper

On Fri, May 27, 2016 at 9:19 AM, Jamal notifications@github.com wrote:

Thank you for your reply. Could you please tell me the best package to normalize the genotyping array? Regards, Jamal

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Elkoumy commented 8 years ago

Thank you.