[aroma.affymetrix] Re: FIRMAGene command
Unfortunately I cannot get to the docs, unless the same docs are stored under help.start() I used following parameters: plm - RmaPlm(csNU) plm [1] RmaPlm: 0x22388540 cls-gsub(TisMap_,,gsub(_0(1-3)_v1_WTGene1,,getNames(cs))) cls [1] P.L_10 P.L_11 P.L_12 P.L_14 P.L_15 P.L_16 P.L_2 P.L_3 [9] P.L_4 P.L_5 P.L_6 P.L_7 P.L_8 P.L_9 I am not sure what is supposed to be stored in cls and u. I’m a bit confused however, with what the whole “unique cdf set” is for and how plm is working. Can I save the plm data into a txt file? Many thanks for your help. I really appreciate it. Daniela On Mar 16, 4:57 pm, Mark Robinson mrobin...@wehi.edu.au wrote: Hi Daniela. You haven't told us what inputs you've used for 'plm' and 'cls' ... and what is stored in 'u'? Have you read the docs at: ?FIRMAGene Cheers, Mark On 14-Mar-10, at 10:21 AM, dkny169 wrote: Hello, I have a question regarding FIRMAGene. Executing the FIRMAGene command I get the following error: fg-FIRMAGene(plm, idsToUse=u, cls=cls) Gathering/calculating residuals. Reading units. Error in if (any(units 1)) stop(Argument 'units' contains non- positive indices.) : missing value where TRUE/FALSE needed The commands used right before are: monetaffx-read.csv(MoEx-1_0-st-v1.na29.mm9.transcript.csv, sep=,,skip=20, header=TRUE,comment.char=,stringsAsFactors=FALSE) probetab-read.table(MoEx-1_0-st-v1.na29.mm9.probeset.csv, sep=\t, header=TRUE, comment.char=, stringsAsFactors=FALSE) u-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx $category ==main monetaffx$total_probes 7 monetaffx $total_probes 200]) I'm not sure what these commands do and how they need to be changed to accommodate my own data: cls - gsub(TisMap_,,gsub(_0[1-3]_v1_WTGene1,,getNames(cs))) Many thanks, Daniela -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group athttp://groups.google.com/group/aroma-affymetrix?hl=en -- Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 -- __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __ -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
[aroma.affymetrix] Re: FIRMAGene command
I definitely loaded the package and had a look at the help.start docs. Neverthelss, I wasn't able to work out my problems that I described in my previous post. On Mar 18, 1:58 pm, Henrik Bengtsson henrik.bengts...@gmail.com wrote: Hi. On Thu, Mar 18, 2010 at 6:47 PM, dkny169 daniela...@yahoo.com wrote: Unfortunately I cannot get to the docs, unless the same docs are stored under help.start() Please explain what the problem/error is. Note that you have to load a package in order to use ?/help() on its methods, e.g. library(FIRMAGene); ?FIRMAGene If you don't load it, you get something like: ?FIRMAGene No documentation for 'FIRMAGene' in specified packages and libraries: you could try '??FIRMAGene' The help is the same regardless if you access it via ?/help() or help.start(). So, yes, you'll find the same information if you do help.start() - Packages - FIRMAGene - FIRMAGene /Henrik I used following parameters: plm - RmaPlm(csNU) plm [1] RmaPlm: 0x22388540 cls-gsub(TisMap_,,gsub(_0(1-3)_v1_WTGene1,,getNames(cs))) cls [1] P.L_10 P.L_11 P.L_12 P.L_14 P.L_15 P.L_16 P.L_2 P.L_3 [9] P.L_4 P.L_5 P.L_6 P.L_7 P.L_8 P.L_9 I am not sure what is supposed to be stored in cls and u. I’m a bit confused however, with what the whole “unique cdf set” is for and how plm is working. Can I save the plm data into a txt file? Many thanks for your help. I really appreciate it. Daniela On Mar 16, 4:57 pm, Mark Robinson mrobin...@wehi.edu.au wrote: Hi Daniela. You haven't told us what inputs you've used for 'plm' and 'cls' ... and what is stored in 'u'? Have you read the docs at: ?FIRMAGene Cheers, Mark On 14-Mar-10, at 10:21 AM, dkny169 wrote: Hello, I have a question regarding FIRMAGene. Executing the FIRMAGene command I get the following error: fg-FIRMAGene(plm, idsToUse=u, cls=cls) Gathering/calculating residuals. Reading units. Error in if (any(units 1)) stop(Argument 'units' contains non- positive indices.) : missing value where TRUE/FALSE needed The commands used right before are: monetaffx-read.csv(MoEx-1_0-st-v1.na29.mm9.transcript.csv, sep=,,skip=20, header=TRUE,comment.char=,stringsAsFactors=FALSE) probetab-read.table(MoEx-1_0-st-v1.na29.mm9.probeset.csv, sep=\t, header=TRUE, comment.char=, stringsAsFactors=FALSE) u-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx $category ==main monetaffx$total_probes 7 monetaffx $total_probes 200]) I'm not sure what these commands do and how they need to be changed to accommodate my own data: cls - gsub(TisMap_,,gsub(_0[1-3]_v1_WTGene1,,getNames(cs))) Many thanks, Daniela -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group athttp://groups.google.com/group/aroma-affymetrix?hl=en -- Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 -- __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __ -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group athttp://groups.google.com/group/aroma-affymetrix?hl=en -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at
Re: [aroma.affymetrix] Re: FIRMAGene command
Hi Daniela. I definitely loaded the package and had a look at the help.start docs. Neverthelss, I wasn't able to work out my problems that I described in my previous post. OK, so you've read the documentation. But, you haven't told us what you didn't understand there. I can try and explain the docs to you ... - cls: variable giving the class (aligned with the columns or sample names of the input object). - So, this says that you need to specify a vector which gives the experimental group of your samples. So, in my example, the sample names were: getNames(cs) [1] TisMap_Brain_01_v1_WTGene1TisMap_Brain_02_v1_WTGene1 [3] TisMap_Brain_03_v1_WTGene1TisMap_Breast_01_v1_WTGene1 [5] TisMap_Breast_02_v1_WTGene1 TisMap_Breast_03_v1_WTGene1 [snip] which get converted to: cls-gsub(TisMap_,,gsub(_0[1-3]_v1_WTGene1,,getNames(cs))) cls [1] BrainBrainBrainBreast Breast Breast [snip] And, with the 'cls' variable, I tell FIRMAGene() what group each sample is from. You need to do the same for you 14 samples. --- idsToUse: indices of the units to calculate FIRMAGene scores for. --- In my example, all this does: u - which(getUnitNames(cdf) %in% hgnetaffx$probeset_id[hgnetaffx$category == main hgnetaffx$total_probes 7 hgnetaffx$total_probes 200]) ... (assuming you've read in an appropriate file to hgnetaffx) ... only uses the main category probeset (i.e. not the control probesets), only probesets with 7 and 200 probes within them. I am not sure what is supposed to be stored in cls and u. OK, so hopefully you are ok with whats spelled out above. Ask questions, mentioning what you don't understand, if not. I’m a bit confused however, with what the whole “unique cdf set” is for and how plm is working. Can I save the plm data into a txt file? You don't really need to understand the uniquifying. Its just a step that needs to be done. For general info on probe level models, you might look at the references mentioned in fitPLM() or rma(): library(affyPLM) ?fitPLM library(oligo) ?rma In terms of saving the plm data (I assume you mean chip effects?), you should breeze through the vignette for Gene 1.0 ST arrays. At the end, it extracts the summarized data into a data frame: http://aroma-project.org/node/38 ... and you could output this to a text file using write.table(). Hope that helps. Cheers, Mark On Fri, Mar 19, 2010 at 5:25 AM, dkny169 daniela...@yahoo.com wrote: I definitely loaded the package and had a look at the help.start docs. Neverthelss, I wasn't able to work out my problems that I described in my previous post. On Mar 18, 1:58 pm, Henrik Bengtsson henrik.bengts...@gmail.com wrote: Hi. On Thu, Mar 18, 2010 at 6:47 PM, dkny169 daniela...@yahoo.com wrote: Unfortunately I cannot get to the docs, unless the same docs are stored under help.start() Please explain what the problem/error is. Note that you have to load a package in order to use ?/help() on its methods, e.g. library(FIRMAGene); ?FIRMAGene If you don't load it, you get something like: ?FIRMAGene No documentation for 'FIRMAGene' in specified packages and libraries: you could try '??FIRMAGene' The help is the same regardless if you access it via ?/help() or help.start(). So, yes, you'll find the same information if you do help.start() - Packages - FIRMAGene - FIRMAGene /Henrik I used following parameters: plm - RmaPlm(csNU) plm [1] RmaPlm: 0x22388540 cls-gsub(TisMap_,,gsub(_0(1-3)_v1_WTGene1,,getNames(cs))) cls [1] P.L_10 P.L_11 P.L_12 P.L_14 P.L_15 P.L_16 P.L_2 P.L_3 [9] P.L_4 P.L_5 P.L_6 P.L_7 P.L_8 P.L_9 I am not sure what is supposed to be stored in cls and u. I’m a bit confused however, with what the whole “unique cdf set” is for and how plm is working. Can I save the plm data into a txt file? Many thanks for your help. I really appreciate it. Daniela On Mar 16, 4:57 pm, Mark Robinson mrobin...@wehi.edu.au wrote: Hi Daniela. You haven't told us what inputs you've used for 'plm' and 'cls' ... and what is stored in 'u'? Have you read the docs at: ?FIRMAGene Cheers, Mark On 14-Mar-10, at 10:21 AM, dkny169 wrote: Hello, I have a question regarding FIRMAGene. Executing the FIRMAGene command I get the following error: fg-FIRMAGene(plm, idsToUse=u, cls=cls) Gathering/calculating residuals. Reading units. Error in if (any(units 1)) stop(Argument 'units' contains non- positive indices.) : missing value where TRUE/FALSE needed The commands used right before are: monetaffx-read.csv(MoEx-1_0-st-v1.na29.mm9.transcript.csv, sep=,,skip=20, header=TRUE,comment.char=,stringsAsFactors=FALSE) probetab-read.table(MoEx-1_0-st-v1.na29.mm9.probeset.csv, sep=\t, header=TRUE, comment.char=, stringsAsFactors=FALSE) u-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx $category ==main
[aroma.affymetrix] Re: FIRMAGene with masked CEL files
Hi Mark, Thanks very much for the feedback. In the spirit of completeness I tried upgrading aroma.affymetrix and emptying the caches, although given your reply I'm not surprised it didn't work (see attached). I'll try with the custom CDF file approach and let you know how I get on. Cheers, Tim traceback() 10: .C(muf, v = as.double(v), x = as.double(x), n = as.integer(n), PACKAGE = FIRMAGene) 9: mufC(x) 8: FUN(newX[, i], ...) 7: apply(d, 2, mufMax) 6: mufColumns(u) 5: FUN(X[[11L]], ...) 4: lapply(X, FUN, ...) 3: sapply(rsu1[w], FUN = function(u) mufColumns(u)) 2: t(sapply(rsu1[w], FUN = function(u) mufColumns(u))) 1: FIRMAGene(plm, idsToUse = u, cls = cls) sessionInfo() R version 2.10.0 Patched (2009-11-03 r50305) x86_64-apple-darwin9.8.0 locale: [1] en_GB/en_GB/C/C/en_GB/en_GB attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] FIRMAGene_0.9.5preprocessCore_1.8.0 [3] genefilter_1.28.0 SmithLabArray_0.3.7 [5] cluster_1.12.1 hugene10stv1exoncdf_1.22.0 [7] Biobase_2.6.0 aroma.affymetrix_1.3.0 [9] aroma.apd_0.1.7affxparser_1.18.0 [11] R.huge_0.2.0 aroma.core_1.3.1 [13] aroma.light_1.14.0 matrixStats_0.1.8 [15] R.rsp_0.3.6R.filesets_0.6.5 [17] digest_0.4.1 R.cache_0.2.0 [19] R.utils_1.2.4 R.oo_1.6.5 [21] affy_1.24.2R.methodsS3_1.0.3 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1 [4] DBI_0.2-4 gdata_2.6.1 gplots_2.7.4 [7] grid_2.10.0 gtools_2.6.1hopach_2.6.0 [10] lattice_0.17-26 limma_3.2.1 RColorBrewer_1.0-2 [13] RCurl_1.2-1 RSQLite_0.7-3 splines_2.10.0 [16] survival_2.35-7 tools_2.10.0vsn_3.14.0 [19] XML_2.6-0 xtable_1.5-6 On Nov 17, 1:18 am, Mark Robinson mrobin...@wehi.edu.au wrote: Hi Tim. The FIRMAGene code is not designed to play nice with NAs in the probe level data. I'm somewhat hesitant to include this because it would require making assumptions about how people have introduced NAs into their CEL files. If you want to exclude a subset of the standard collection of probes, a more elegant solution is to create a CDF file (e.g. with a tag) that only uses the probes you want to use. I'm interested to know what affect this has on your results, so do keep me posted. Cheers, Mark On 17-Nov-09, at 3:59 AM, Henrik Bengtsson wrote: Hi. Update aroma.affymetrix to v1.3.0 and report back. If/when you get the error, please also report what traceback() outputs. /Henrik PS. I'm even surprised that you got this far because the version you have now is not compatible with the R.filesets version you have. On Mon, Nov 16, 2009 at 5:48 PM, Tim Rayner tfray...@gmail.com wrote: Hi, I've been experimenting with using FIRMAGene to detect differential splicing, and while the package seems to be working well we're seeing quite a lot of splicing events which we think are due to poorly- detected probes on the array. I've been trying to filter these probes out by identifying them with the APT DABG algorithm and then setting those probe signals to NA in the CEL files. I used the method suggested here to do this: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/... . This all seems to work well enough, but when I then try and use these files downstream in FIRMAGene, I get the following error (csNU is the filtered data set): plm - RmaPlm(csNU) fit(plm, verbose=verbose) fg - FIRMAGene(plm, idsToUse=u, cls=cls) Gathering/calculating residuals. Reading units. Extracting standardized residuals. used (Mb) gc trigger (Mb) max used (Mb) Ncells 7119728 380.3 10591793 565.7 10591793 565.7 Vcells 55053141 420.1 130562333 996.2 130551609 996.1 Calculating MUF score (observed data). 28133 Error in mufC(x) : NA/NaN/Inf in foreign function call (arg 1) My sessionInfo is as follows: sessionInfo() R version 2.10.0 Patched (2009-11-03 r50305) x86_64-apple-darwin9.8.0 locale: [1] en_GB/en_GB/C/C/en_GB/en_GB attached base packages: [1] grDevices datasets utils graphics stats methods base other attached packages: [1] FIRMAGene_0.9.5 hugene10stv1exoncdf_1.22.0 [3] genefilter_1.28.0 SmithLabArray_0.3.7 [5] aroma.affymetrix_1.2.0 aroma.apd_0.1.7 [7] affxparser_1.18.0 R.huge_0.2.0 [9] aroma.core_1.2.0 aroma.light_1.14.0 [11] matrixStats_0.1.6 R.rsp_0.3.6 [13] R.filesets_0.6.5 digest_0.4.1 [15] R.cache_0.2.0 R.utils_1.2.4 [17] R.oo_1.6.5 R.methodsS3_1.0.3 [19] Biobase_2.6.0 cluster_1.12.1 loaded via a namespace (and not attached): [1] affy_1.24.2 affyio_1.14.0
[aroma.affymetrix] Re: FIRMAGene
Dear Mark, I'm wondering whether there is relationship between the array quality, in terms of NUSE (and RLE?) plot, and the FIRMAGene scores. Do you expect that a low quality array will show higher FIRMAGene scores respect to a high quality array? Indeed, from preliminary analysis, it seems that this is the case. Thanks, Ettore M. On Jun 11, 3:10 pm, Mark Robinson mrobin...@wehi.edu.au wrote: Hi Nick. At present, FIRMAGene is not actually part of the aroma.affymetrix project, although it makes use of it. So, I will reply to this off the aroma.affymetrix mailing list, except to say that FIRMAGene is now hosted by R-forge. See the following link for details: http://bioinf.wehi.edu.au/folders/firmagene/ When (and if) time permits, I plan to add FIRMAGene to aroma.affymetrix, so that it can share the same memory efficiency and mailing list support. Cheers, Mark On 11/06/2009, at 10:31 PM, nmcgli...@googlemail.com wrote: Hello, I have two questions regarding FIRMAGene: 1. The same as the first in this thread: using the code from sup3.r when I try to load the FIRMAGene library or execute the FIRMAGene command I get the following errors: library(FIRMAGene) Error in base::library(...) : there is no package called 'FIRMAGene' fg - FIRMAGene(plm, idsToUse=u) Error: could not find function FIRMAGene I'm using aroma.affymetrix v1.1.0 with R2.9.0 on MacOSX 10.5.7 2. I'm unsure of what this command is doing and how it needs to be changed to accommodate my own data: cls - gsub(TisMap_,,gsub(_0[1-3]_v1_WTGene1,,getNames(cs))) Many thanks, Nick -- Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 -- --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: FIRMAGene
Hello, I have two questions regarding FIRMAGene: 1. The same as the first in this thread: using the code from sup3.r when I try to load the FIRMAGene library or execute the FIRMAGene command I get the following errors: library(FIRMAGene) Error in base::library(...) : there is no package called 'FIRMAGene' fg - FIRMAGene(plm, idsToUse=u) Error: could not find function FIRMAGene I'm using aroma.affymetrix v1.1.0 with R2.9.0 on MacOSX 10.5.7 2. I'm unsure of what this command is doing and how it needs to be changed to accommodate my own data: cls - gsub(TisMap_,,gsub(_0[1-3]_v1_WTGene1,,getNames(cs))) Many thanks, Nick --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: FIRMAGene
Hi Nick. At present, FIRMAGene is not actually part of the aroma.affymetrix project, although it makes use of it. So, I will reply to this off the aroma.affymetrix mailing list, except to say that FIRMAGene is now hosted by R-forge. See the following link for details: http://bioinf.wehi.edu.au/folders/firmagene/ When (and if) time permits, I plan to add FIRMAGene to aroma.affymetrix, so that it can share the same memory efficiency and mailing list support. Cheers, Mark On 11/06/2009, at 10:31 PM, nmcgli...@googlemail.com wrote: Hello, I have two questions regarding FIRMAGene: 1. The same as the first in this thread: using the code from sup3.r when I try to load the FIRMAGene library or execute the FIRMAGene command I get the following errors: library(FIRMAGene) Error in base::library(...) : there is no package called 'FIRMAGene' fg - FIRMAGene(plm, idsToUse=u) Error: could not find function FIRMAGene I'm using aroma.affymetrix v1.1.0 with R2.9.0 on MacOSX 10.5.7 2. I'm unsure of what this command is doing and how it needs to be changed to accommodate my own data: cls - gsub(TisMap_,,gsub(_0[1-3]_v1_WTGene1,,getNames(cs))) Many thanks, Nick -- Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 -- --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: FIRMAGene
I have the following question. In the sup3.R file the probe level model fitting is realised using the instructions: plm - RmaPlm(csNU) fit(plm, verbose=verbose) where csNU is an object obtained after background correction, quantile normalisation and conversion of the cdf to a unique version. I suppose that this approach should enable the exon-level analysis of the Gene 1.0 data, as required by FIRMAGene. However I don't understand where is the difference since the methods are the same as in the gene-level analysis of such data. Thanks, Ettore M. On May 29, 3:16 pm, rhizomorph cognitiontechnic...@yahoo.com wrote: I have the same question as Ettore. I installed the aroma.affymetrix package (and all supporting packages), but nowhere can I find a source to download and install the FIRMAGene package that the SUP3.R script clearly calls for. Rhizomorph. On May 29, 3:15 am, ettore mosca ettore.mos...@gmail.com wrote: Dear aroma.affymetrix developers, I'm very interested in using Gene 1.0 ST platform for alternative splicing. I read in your paper Differential splicing using whole-transcript microarrays that FIRMAGene is freely available as R package but I can not load the library following the instruction in the third additional file sup3.r (I installed and loaded aroma.affymetrix successfully) How do I install and load FIRMAGene library? Thanks, Ettore M. -- Ettore M. http://www.ettoremosca.it --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: FIRMAGene
Hi Ettore. Comments below. I have the following question. In the sup3.R file the probe level model fitting is realised using the instructions: plm - RmaPlm(csNU) fit(plm, verbose=verbose) where csNU is an object obtained after background correction, quantile normalisation and conversion of the cdf to a unique version. The conversion to 'unique' is actually done both on the CDF and the data. This is simply to dance around the fact that a handful of probes are used in multiple probesets. I suppose that this approach should enable the exon-level analysis of the Gene 1.0 data, as required by FIRMAGene. However I don't understand where is the difference since the methods are the same as in the gene-level analysis of such data. I'm actually not sure what it is you are asking here. Indeed, the methodology of FIRMAGene operates on the results (specifically, the residuals) of your standard RMA probe level model. This is, however, quite different to the standard DE analysis, if that is what you mean by gene-level analysis. Hope that helps. Cheers, Mark Thanks, Ettore M. On May 29, 3:16 pm, rhizomorph cognitiontechnic...@yahoo.com wrote: I have the same question as Ettore. I installed the aroma.affymetrix package (and all supporting packages), but nowhere can I find a source to download and install the FIRMAGene package that the SUP3.R script clearly calls for. Rhizomorph. On May 29, 3:15 am, ettore mosca ettore.mos...@gmail.com wrote: Dear aroma.affymetrix developers, I'm very interested in using Gene 1.0 ST platform for alternative splicing. I read in your paper Differential splicing using whole-transcript microarrays that FIRMAGene is freely available as R package but I can not load the library following the instruction in the third additional file sup3.r (I installed and loaded aroma.affymetrix successfully) How do I install and load FIRMAGene library? Thanks, Ettore M. -- Ettore M. http://www.ettoremosca.it --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
