Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects
On Thu, Dec 11, 2014 at 4:52 AM, Rishi Das Roy rishi.das...@gmail.com wrote: Hi Thanks for your reply. I can understand that I can identify alternative splicing through FIRMA more confidently. However I also want to identify differentially expressed genes. I have not find any documentation regarding this in aroma-project.org . Please provide any example to find DE genes through aroma.affymetrix. If you look at http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis, you find the following passages: There are two options, regardless of the kind of custom CDF you use. To fit a summary of the entire transcript (i.e. estimate the overall expression for the transcript), do: plmTr - ExonRmaPlm(csN, mergeGroups=TRUE) print(plmTr) and then a bit later also: To extract the estimates (transcript or probeset) use either extractMatrix() or extractDataFrame() on the ChipEffectSet that corresponds to the plm object: cesTr - getChipEffectSet(plmTr) trFit - extractDataFrame(cesTr, units=1:3, addNames=TRUE) This will give a data.frame with three rows, each row corresponding to a unit/transcript. Hope this helps Henrik Thanks rishi On Wednesday, December 10, 2014 11:39:50 PM UTC+2, Henrik Bengtsson wrote: Hi, you cannot use RMA on exon-arrays, you will need to use exon-aware method such as FIRMA (e.g. http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis). Hope this helps Henrik PS. For http://aroma-project.org/replication/RMA, I've updated it to use `theta - extractTheta(ces)` instead of `theta - extractMatrix(ces)`. This will allow you to set the row names. But as you'll find out, 'theta' becomes an JxKxI array for exon-arrays, where J is the number of genes, I is the number of samples and K is the maximum number of exons per gene found. In other words, using doRMA() on exon arrays gives you at best exon-specific estimates (and they are not very good estimates - FIRMA is doing a much better job on that). On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy rishi@gmail.com wrote: Hi, I was trying to perform RMA on Mouse Exon 1.0 ST Array as described in aroma website (link) using custom cdf MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz . I have executed following code in R cdf - AffymetrixCdfFile$byChipType(chipType, tags=coreR1,A20080718,MR) cs - AffymetrixCelSet$byName(data_CEL, cdf=cdf); bc - RmaBackgroundCorrection(cs); csB - process(bc); qn - QuantileNormalization(csB, typesToUpdate=pm); csN - process(qn); plm - RmaPlm(csN); fit(plm); ces - getChipEffectSet(plm); theta - extractMatrix(ces); rownames(theta) - getUnitNames(cdf); Error in `rownames-`(`*tmp*`, value = c(6838637, 6992377, 6901592, : length of 'dimnames' [1] not equal to array extent Please help me to understand this error and how can I solve this. The session info is given below. With regards Rishi R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=fi_FI.UTF-8LC_NUMERIC=CLC_TIME=en_GB LC_COLLATE=en_GBLC_MONETARY=fi_FI.UTF-8 [6] LC_MESSAGES=en_GB LC_PAPER=en_GB LC_NAME=C LC_ADDRESS=CLC_TELEPHONE=C [11] LC_MEASUREMENT=en_GBLC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods base other attached packages: [1] preprocessCore_1.28.0 aroma.light_2.2.0 aroma.affymetrix_2.12.8 aroma.core_2.12.8 [5] R.devices_2.12.0 R.filesets_2.6.0 R.utils_1.34.0R.oo_1.18.2 [9] R.methodsS3_1.6.2 affxparser_1.38.0 pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0 [13] BiocInstaller_1.16.1 pd.moex.1.0.st.v1_3.10.0 RSQLite_1.0.0 DBI_0.3.1 [17] moex10stmmrefseqcdf_19.0.0AnnotationDbi_1.28.1 GenomeInfoDb_1.2.3oligo_1.30.0 [21] Biostrings_2.34.0 XVector_0.6.0 IRanges_2.0.0 S4Vectors_0.4.0 [25] Biobase_2.26.0oligoClasses_1.28.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] affyio_1.34.0aroma.apd_0.5.0 base64enc_0.1-2 bit_1.1-12 codetools_0.2-8 digest_0.6.5 [7] DNAcopy_1.40.0 ff_2.2-13foreach_1.4.2 GenomicRanges_1.18.3 iterators_1.0.7 matrixStats_0.12.2 [13] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0 R.rsp_0.19.6 splines_3.1.2tools_3.1.2 [19] zlibbioc_1.12.0 -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to
[aroma.affymetrix] Encountered ERROR while extracting chip effects
Hi, I was trying to perform RMA on *Mouse Exon 1.0 ST Array* as described in aroma website (link http://www.aroma-project.org/replication/RMA) using custom cdf MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz http://www.aroma-project.org/data/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz . I have executed following code in R cdf - AffymetrixCdfFile$byChipType(chipType, tags=coreR1,A20080718,MR) cs - AffymetrixCelSet$byName(data_CEL, cdf=cdf); bc - RmaBackgroundCorrection(cs); csB - process(bc); qn - QuantileNormalization(csB, typesToUpdate=pm); csN - process(qn); plm - RmaPlm(csN); fit(plm); ces - getChipEffectSet(plm); theta - extractMatrix(ces); rownames(theta) - getUnitNames(cdf); Error in `rownames-`(`*tmp*`, value = c(6838637, 6992377, 6901592, : length of 'dimnames' [1] not equal to array extent Please help me to understand this error and how can I solve this. The session info is given below. With regards Rishi R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=fi_FI.UTF-8LC_NUMERIC=C LC_TIME=en_GB LC_COLLATE=en_GBLC_MONETARY=fi_FI.UTF-8 [6] LC_MESSAGES=en_GB LC_PAPER=en_GB LC_NAME=C LC_ADDRESS=CLC_TELEPHONE=C [11] LC_MEASUREMENT=en_GBLC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods base other attached packages: [1] preprocessCore_1.28.0 aroma.light_2.2.0 aroma.affymetrix_2.12.8 aroma.core_2.12.8 [5] R.devices_2.12.0 R.filesets_2.6.0 R.utils_1.34.0R.oo_1.18.2 [9] R.methodsS3_1.6.2 affxparser_1.38.0 pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0 [13] BiocInstaller_1.16.1 pd.moex.1.0.st.v1_3.10.0 RSQLite_1.0.0 DBI_0.3.1 [17] moex10stmmrefseqcdf_19.0.0AnnotationDbi_1.28.1 GenomeInfoDb_1.2.3oligo_1.30.0 [21] Biostrings_2.34.0 XVector_0.6.0 IRanges_2.0.0 S4Vectors_0.4.0 [25] Biobase_2.26.0oligoClasses_1.28.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] affyio_1.34.0aroma.apd_0.5.0 base64enc_0.1-2 bit_1.1-12 codetools_0.2-8 digest_0.6.5 [7] DNAcopy_1.40.0 ff_2.2-13foreach_1.4.2 GenomicRanges_1.18.3 iterators_1.0.7 matrixStats_0.12.2 [13] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0 R.rsp_0.19.6 splines_3.1.2tools_3.1.2 [19] zlibbioc_1.12.0 -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects
Hi, you cannot use RMA on exon-arrays, you will need to use exon-aware method such as FIRMA (e.g. http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis). Hope this helps Henrik PS. For http://aroma-project.org/replication/RMA, I've updated it to use `theta - extractTheta(ces)` instead of `theta - extractMatrix(ces)`. This will allow you to set the row names. But as you'll find out, 'theta' becomes an JxKxI array for exon-arrays, where J is the number of genes, I is the number of samples and K is the maximum number of exons per gene found. In other words, using doRMA() on exon arrays gives you at best exon-specific estimates (and they are not very good estimates - FIRMA is doing a much better job on that). On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy rishi.das...@gmail.com wrote: Hi, I was trying to perform RMA on Mouse Exon 1.0 ST Array as described in aroma website (link) using custom cdf MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz . I have executed following code in R cdf - AffymetrixCdfFile$byChipType(chipType, tags=coreR1,A20080718,MR) cs - AffymetrixCelSet$byName(data_CEL, cdf=cdf); bc - RmaBackgroundCorrection(cs); csB - process(bc); qn - QuantileNormalization(csB, typesToUpdate=pm); csN - process(qn); plm - RmaPlm(csN); fit(plm); ces - getChipEffectSet(plm); theta - extractMatrix(ces); rownames(theta) - getUnitNames(cdf); Error in `rownames-`(`*tmp*`, value = c(6838637, 6992377, 6901592, : length of 'dimnames' [1] not equal to array extent Please help me to understand this error and how can I solve this. The session info is given below. With regards Rishi R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=fi_FI.UTF-8LC_NUMERIC=CLC_TIME=en_GB LC_COLLATE=en_GBLC_MONETARY=fi_FI.UTF-8 [6] LC_MESSAGES=en_GB LC_PAPER=en_GB LC_NAME=C LC_ADDRESS=CLC_TELEPHONE=C [11] LC_MEASUREMENT=en_GBLC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods base other attached packages: [1] preprocessCore_1.28.0 aroma.light_2.2.0 aroma.affymetrix_2.12.8 aroma.core_2.12.8 [5] R.devices_2.12.0 R.filesets_2.6.0 R.utils_1.34.0R.oo_1.18.2 [9] R.methodsS3_1.6.2 affxparser_1.38.0 pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0 [13] BiocInstaller_1.16.1 pd.moex.1.0.st.v1_3.10.0 RSQLite_1.0.0 DBI_0.3.1 [17] moex10stmmrefseqcdf_19.0.0AnnotationDbi_1.28.1 GenomeInfoDb_1.2.3oligo_1.30.0 [21] Biostrings_2.34.0 XVector_0.6.0 IRanges_2.0.0 S4Vectors_0.4.0 [25] Biobase_2.26.0oligoClasses_1.28.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] affyio_1.34.0aroma.apd_0.5.0 base64enc_0.1-2 bit_1.1-12 codetools_0.2-8 digest_0.6.5 [7] DNAcopy_1.40.0 ff_2.2-13foreach_1.4.2 GenomicRanges_1.18.3 iterators_1.0.7 matrixStats_0.12.2 [13] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0 R.rsp_0.19.6 splines_3.1.2tools_3.1.2 [19] zlibbioc_1.12.0 -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
