Question: FW: URGENT Help required: Getting this error with GAGE analysis, input files attached
0
7.6 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
On 01/26/2012 12:41 PM, Javerjung Sandhu wrote: > Hi Martin, > Thanks for the reply. I am forwarding this message to you which shows > the error in RED. I have checked the help pages for GAGE, readExpData > which don't give that much info. Class of "Micro_array_data" is a > data.frame. I will also forward you the email of Mr. Luo Weijun which The help page ?gage says that class of the first argument should be a 'matrix'. The error message also says that the function was expecting a 'matrix'. As you have discovered you provided a 'data.frame'. Is a data.frame a matrix? Martin > might help you i assume. In that email Mr. Luo Weijun explains what > should be the format of input files and how should i read them. I am > reading the files in the same way but still it shows the error. > Thanks, > Jung > -------------------------------------------------------------------- ---- > *From:* Javerjung Sandhu > *Sent:* Tuesday, January 24, 2012 11:16 AM > *To:* luo_weijun at yahoo.com > *Cc:* bioconductor at r-project.org > *Subject:* URGENT Help required: Getting this error with GAGE analysis, > input files attached. > > > -------------------------------------------------------------------- ---- > *From:* Javerjung Sandhu > *Sent:* Monday, January 23, 2012 1:27 PM > *To:* Valerie Obenchain > *Cc:* bioconductor at r-project.org; luo_weijun at yahoo.com > *Subject:* Getting this error with GAGE analysis, input files attached > > Hi there, > I am getting this error on R console. I have attached the input files. > Help will be really appreciated. > > > Micro_array_data <- readExpData(file = "Micro_array_dataset.txt") > > Gene_set <- readList("Gene_set.gmt") > > Reference_condition <- c(1,3,5) > > Target_condition <- c(2,4,6) > > A1_compare_un <- gage(Micro_array_data, Gene_set, ref = > Reference_condition, samp = Target_condition) > Error in saaPrep(exprs, ref = ref, samp = samp, same.dir = same.dir, > compare = compare, : > exprs needs to be a numeric matrix or vector > > # Essential_member_genes <- essGene(Gene_set, Micro_array_data,ref = > NULL) > > # Non_redundant_significant_gene_set_list <- esset.grp() > > > > Thanks, > > Jung > > ________________________________________ > From: Valerie Obenchain [vobencha at fhcrc.org] > Sent: Monday, January 23, 2012 9:50 AM > To: Javerjung Sandhu > Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE > Analysis and DO a BASIC GAGE analysis using those files > > Hello, > > On 01/22/12 16:31, Javerjung Sandhu wrote: > > Hi Valerie, > > Thanks for the information. Now i won't follow the vignette, i am > trying to write my own code from scratch. > > My supervisor said i should follow the GO.GS gene dataset for now and > we can work with others later. Actually i am an engineering science > student who had no background in biology and i got a co-op job at bc > cancer agency to do some analysis using perl and python. But last month > my supervisor said that i need to work on GAGE therefore i learned the R > from different sources and also from the R website, i got the "R intro" > file which helped me a lot to learn R. > > So i have a request for you. I will send you the code which i will > write along with the data files. So if you could please help me in > getting rid of the errors so that i can finish the analysis asap. > If you have problems using the gage package, they should be posted on > the bioconductor mailing list. As you mentioned, Weijun has also > responded to your message and is willing to help. Posting on the list > makes it possible for more than one person to respond and for other new > users to learn from the discussion. So, once you have your script > written and have tried to use the functions in gage, post them to the > mailing list. You need to provide a small working example of what you > have tried and what errors you are seeing. > > > I really appreciate all your help. > > I also recieved an email from Weijun. I will go through that email > and ask you questions/problems. > > If possible can you write a script for me which can do a basic GAGE > analysis and i can edit that to customise it according to my needs. You > can use the GO.GS gene set and the input file which i have attached > right now. > No, unfortunately I can't write the script for you. The vignette in the > package has examples of how to perform a gage analysis. Your data will > be different but the general steps will be the same. If you run into > trouble, post a small, reproducible example on the mailing list. > > Valerie > > > But i am also writing my code but i am so depressed, sad and > confused; i don't think my code will work. > > Thanks, > > Jung > > > > ________________________________________ > > From: Valerie Obenchain [vobencha at fhcrc.org] > > Sent: Thursday, January 19, 2012 5:54 PM > > To: Javerjung Sandhu > > Cc: bioconductor at r-project.org; luo_weijun at yahoo.com > > Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE > Analysis and DO a BASIC GAGE analysis using those files > > > > Hi Jung, > > > > Thank you for sending your files but there is no need to attach the > > source files from the gage package (GAGE.r, gage.pdf). I have access to > > those files. > > > > The package vignette is just intended to be an example. Clearly the data > > in the package and your data will be very different. It does not make > > sense to try to follow the code exactly "as is" when using your data. > > For example, it doesn't make sense for you to grep for 'HN', 'ADH' and > > 'DCIS' since they don't exist in your file. These are treatment groups > > included in the gage sample data and have no bearing on your analysis. > > This is why you see nothing (i.e., integer(0)) for these variables. > > > > > Micro_array_dataset<- read.table("Micro_array_dataset.txt") > > > cn=colnames(Micro_array_dataset) > > > hn=grep('HN',cn, ignore.case =T) > > > adh=grep('ADH',cn, ignore.case =T) > > > dcis=grep('DCIS',cn, ignore.case =T) > > > print(hn) > > integer(0) > > > print(dcis) > > integer(0) > > > > > > This error is due to the fact that you are subsetting a data.frame and > > have not specified the columns. In the vignette, the gene set is a list > > so this subsetting works. > > > > > lapply(Gene_set[1:3],head) > > Error in [.data.frame(Gene_set, 1:3) : undefined columns selected > > > > > > Next, your genes need to be grouped by pathway. The idea is to do an > > analysis of gene pathways so you need to provide a list of genes grouped > > by pathway (like the kegg.gs or go.gs example files in the vignette). > > Your gene file consists only of gene names, > > > > > head(rownames(Micro_array_dataset)) > > [1] "ENSG00000000003" "ENSG00000000005" "ENSG00000000419" > "ENSG00000000457" > > [5] "ENSG00000000460" "ENSG00000000938" > > > > In R, a list of genes grouped by pathway would look like something like > > this, > > > headkegg.gs) > > $hsa00010 Glycolysis / Gluconeogenesis > > [1] "10327" "124" "125" "126" "127" "128" "130" > > "130589" > > [9] "131" "160287" "1737" "1738" "2023" "2026" "2027" "217" > > ... > > > >$hsa00020 Citrate cycle (TCA cycle) > > [1] "1431" "1737" "1738" "1743" "2271" "283398" "3417" "3418" > > [9] "3419" "3420" "3421" "4190" "4191" "47" "48" "4967" > > ... > > > > You need to identify what pathways you are interested and group the > > genes by those pathways. For identifying pathways take a look at the > > GO.db, KEGG.db or reactome.db. Mapping between gene identifiers can be > > done with the org.*.db packages. > > > > http://www.bioconductor.org/packages/release/data/annotation/ > > > > Some general background on using Bioconductor annotation data is here, > > > > > > > http://www.bioconductor.org/help/workflows/annotation-data /#annotation-resources > > > > > > Valerie > > > > > > On 01/17/12 12:51, Javerjung Sandhu wrote: > >> Hello Valerie, > >> Thanks for your help. I am sending you the data > >> files(Micro_array_dataset.txt**& Gene_Set.txt) which i want to use > >> for the analysis. > >> I need to know in which format the files should be saved (like > >> > http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Da ta_formats > >> this site explains in great detail, what should be the format of the > >> data files required for GSEA analysis (though i am not using GSEA > >> analysis or these file types), same way i want to know in which format > >> i should save the data files required for GAGE analysis so that the > >> analysis is done properly) > >> Please tell me which information is missing from these files. > >> * Yes i know that "gse16873" is expression data and "kegg.gs" is a > >> geneset but i want to use my own, these ones are provided by the author. > >> 1) What i want to accomplish is: I want to do a basic gage analysis > >> (as given in the R script file named "GAGE.r" and pdf file "gage.pdf") > >> such as t-test, rank test, KS test etc. > >> 2) I copied the begining code(to make sure that it loads all the files > >> successfully) from R script file provided by the author (which is also > >> attached as GAGE.r) and made some changes to it and saved as my own > >> script (also attached as Gage_run.r). I tried to load the data files > >> (Micro_array_dataset.txt& Gene_Set.txt) and got these errors (shown > >> in "R Console.txt" file). > >> 3) I run the R script file (Gage_run.r) first to see that it loads all > >> the input files successfully and then i can move ahead with the tests. > >> The output is shown in "R Console.txt" file which shows the errors and > >> warnings. > >> If you need more additional information. Please do tell me. I will be > >> happy to provide that. > >> **an expression matrix with genes as rows and samples as columns. > >> Thanks, > >> Jung > >> ---------------------------------------------------------------- -------- > >> *From:* Valerie Obenchain [vobencha at fhcrc.org] > >> *Sent:* Tuesday, January 17, 2012 10:04 AM > >> *To:* Javerjung Sandhu > >> *Cc:* bioconductor at r-project.org; luo_weijun at yahoo.com > >> *Subject:* Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE > >> Analysis and DO a BASIC GAGE analysis using those files > >> > >> Hello, > >> > >> I think the vignette is clear that you need (1) a gene set and (2) a > >> mircoarray dataset to run the gage analysis. On page 4 they mention > >> the importance of having the same ID system for your gene set and > >> expression data. Once this is accomplished you can use the gage() > >> function. > >> > >> ## this is the expression data > >> gse16873 > >> > >> ## this is the gene set > >> kegg.gs > >> > >> ## call to gage() using 'HN' as control and 'DCIS' as treatment > >> gse16873.kegg.p<- gage(gse16873, gsets = kegg.gs, > >> ref = hn, samp = dcis) > >> > >> > >> I belive if you have only one column of expression data the 'ref' and > >> 'samp' arguments should be omitted (i.e., default of NULL). Read ?gage > >> for details. Maybe the package author will comment on this. I've cc'd > >> them on this message. > >> > >> It is still not clear to me what you have tried. It would be helpful > >> to know the following, > >> > >> (1) what is your analysis question (what are you trying to accomplish) > >> (2) what have you tried (what functions have you used) > >> (3) what errors have you seen from #2 > >> > >> > >> Valerie > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> On 01/16/2012 04:19 PM, Javerjung Sandhu wrote: > >>> Hi Valerie, > >>> First of all thanks a lot for replying and helping me. I really > appreciate that. I am sending you the R source code file which the GAGE > analysis uses plus two other documents which explains what that package > does. > >>> These are the data files used by the GAGE analysis: > >>> ---------------------------- > >>> Data sets in package ?gage?: > >>> carta.gs Common gene set data collections > >>> egSymb Mapping between Entrez Gene IDs and official > >>> symbols > >>> go.gs Common gene set data collections > >>> gse16873 GSE16873: a breast cancer microarray dataset > >>> kegg.gs Common gene set data collections > >>> ----------------------------------------------------- > >>> I have only ONE tab delimited data file in the form of a MATRIX > giving the gene expressions for 173 patients(as columns) and names of > genes(as rows). > >>> I want to know how can i use this package and my data to do the > GAGE analysis. > >>> If you need more information, please tell me. I will be ready to > provide that. > >>> Thanks, > >>> Jung > >>> > >>> ________________________________________ > >>> From: Valerie Obenchain [vobencha at fhcrc.org] > >>> Sent: Monday, January 16, 2012 3:18 PM > >>> To: Javerjung Sandhu > >>> Cc:bioconductor at r-project.org;luo_weijun at yahoo.com > >>> Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for > GAGE Analysis and DO a BASIC GAGE analysis using those files > >>> > >>> Hi Jung, > >>> > >>> Please provide the code you've tried and the error you are seeing. For > >>> example, did you read your own data into R, then try to use gage() and > >>> got an error? We can better help you if we understand your inputs and > >>> the function you're having trouble with. > >>> > >>> Valerie > >>> > >>> > >>> On 01/13/12 13:10, Javerjung Sandhu wrote: > >>>> Dear List, > >>>> I will highly appreciate your help on this. > >>>> For the GAGE analysis package shown by the link given below: > >>>> http://www.bioconductor.org/packages/release/bioc/html/gage.html > >>>> Could you please tell me how to prepare the Custom INPUT files > required for this analysis > >>>> OR > >>>> Send me the SAMPLE DATA files in TXT format so that i know in > which format i need to put the data& how could i DO a BASIC GAGE > analysis using those files. I couldn't figure it out and trying it since > 3 weeks or more. > >>>> Best Regards, > >>>> Jung > >>>> > >>>> [[alternative HTML version deleted]] > >>>> > >>>> _______________________________________________ > >>>> Bioconductor mailing list > >>>> Bioconductor at r-project.org > >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>> Search the > archives:http://news.gmane.org/gmane.science.biology.informatics.con ductor > > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
modified 7.6 years ago by Javerjung Sandhu200 • written 7.6 years ago by Martin Morgan ♦♦ 23k
Answer: FW: URGENT Help required: Getting this error with GAGE analysis, input files att
0
7.6 years ago by
Javerjung Sandhu200 wrote:
Hi Martin, Thanks for the super quick reply. Now i am getting this error.Why i am getting this error. > #!/usr/bin/R > library(gage) > Micro_array_data <- data.matrix(readExpData(file = "Micro_array_dataset.txt")) > Gene_set <- readList("c1_all_v3_0_symbols.gmt") > Reference_condition <- c(1,3,5) > Target_condition <- c(2,4,6) > A1_compare_un <- gage(exprs = Micro_array_data, gsets = Gene_set, ref = Reference_condition, samp = Target_condition ,set.size = c(10,50)) Error in if is.na(spval[i])) tmp[i] <- NA : argument is of length zero > # Essential_member_genes <- essGene(Gene_set, Micro_array_data,ref = NULL) > # Non_redundant_significant_gene_set_list <- esset.grp() > class(Micro_array_data) [1] "matrix" > Thanks, Jung ________________________________________ From: Martin Morgan [mtmorgan@fhcrc.org] Sent: Thursday, January 26, 2012 1:22 PM To: Javerjung Sandhu Cc: bioconductor@r-project.org; luo_weijun@yahoo.com Subject: Re: FW: URGENT Help required: Getting this error with GAGE analysis, input files attached On 01/26/2012 12:41 PM, Javerjung Sandhu wrote: > Hi Martin, > Thanks for the reply. I am forwarding this message to you which shows > the error in RED. I have checked the help pages for GAGE, readExpData > which don't give that much info. Class of "Micro_array_data" is a > data.frame. I will also forward you the email of Mr. Luo Weijun which The help page ?gage says that class of the first argument should be a 'matrix'. The error message also says that the function was expecting a 'matrix'. As you have discovered you provided a 'data.frame'. Is a data.frame a matrix? Martin > might help you i assume. In that email Mr. Luo Weijun explains what > should be the format of input files and how should i read them. I am > reading the files in the same way but still it shows the error. > Thanks, > Jung > -------------------------------------------------------------------- ---- > *From:* Javerjung Sandhu > *Sent:* Tuesday, January 24, 2012 11:16 AM > *To:* luo_weijun@yahoo.com > *Cc:* bioconductor@r-project.org > *Subject:* URGENT Help required: Getting this error with GAGE analysis, > input files attached. > > > -------------------------------------------------------------------- ---- > *From:* Javerjung Sandhu > *Sent:* Monday, January 23, 2012 1:27 PM > *To:* Valerie Obenchain > *Cc:* bioconductor@r-project.org; luo_weijun@yahoo.com > *Subject:* Getting this error with GAGE analysis, input files attached > > Hi there, > I am getting this error on R console. I have attached the input files. > Help will be really appreciated. > > > Micro_array_data <- readExpData(file = "Micro_array_dataset.txt") > > Gene_set <- readList("Gene_set.gmt") > > Reference_condition <- c(1,3,5) > > Target_condition <- c(2,4,6) > > A1_compare_un <- gage(Micro_array_data, Gene_set, ref = > Reference_condition, samp = Target_condition) > Error in saaPrep(exprs, ref = ref, samp = samp, same.dir = same.dir, > compare = compare, : > exprs needs to be a numeric matrix or vector > > # Essential_member_genes <- essGene(Gene_set, Micro_array_data,ref = > NULL) > > # Non_redundant_significant_gene_set_list <- esset.grp() > > > > Thanks, > > Jung > > ________________________________________ > From: Valerie Obenchain [vobencha@fhcrc.org] > Sent: Monday, January 23, 2012 9:50 AM > To: Javerjung Sandhu > Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE > Analysis and DO a BASIC GAGE analysis using those files > > Hello, > > On 01/22/12 16:31, Javerjung Sandhu wrote: > > Hi Valerie, > > Thanks for the information. Now i won't follow the vignette, i am > trying to write my own code from scratch. > > My supervisor said i should follow the GO.GS gene dataset for now and > we can work with others later. Actually i am an engineering science > student who had no background in biology and i got a co-op job at bc > cancer agency to do some analysis using perl and python. But last month > my supervisor said that i need to work on GAGE therefore i learned the R > from different sources and also from the R website, i got the "R intro" > file which helped me a lot to learn R. > > So i have a request for you. I will send you the code which i will > write along with the data files. So if you could please help me in > getting rid of the errors so that i can finish the analysis asap. > If you have problems using the gage package, they should be posted on > the bioconductor mailing list. As you mentioned, Weijun has also > responded to your message and is willing to help. Posting on the list > makes it possible for more than one person to respond and for other new > users to learn from the discussion. So, once you have your script > written and have tried to use the functions in gage, post them to the > mailing list. You need to provide a small working example of what you > have tried and what errors you are seeing. > > > I really appreciate all your help. > > I also recieved an email from Weijun. I will go through that email > and ask you questions/problems. > > If possible can you write a script for me which can do a basic GAGE > analysis and i can edit that to customise it according to my needs. You > can use the GO.GS gene set and the input file which i have attached > right now. > No, unfortunately I can't write the script for you. The vignette in the > package has examples of how to perform a gage analysis. Your data will > be different but the general steps will be the same. If you run into > trouble, post a small, reproducible example on the mailing list. > > Valerie > > > But i am also writing my code but i am so depressed, sad and > confused; i don't think my code will work. > > Thanks, > > Jung > > > > ________________________________________ > > From: Valerie Obenchain [vobencha@fhcrc.org] > > Sent: Thursday, January 19, 2012 5:54 PM > > To: Javerjung Sandhu > > Cc: bioconductor@r-project.org; luo_weijun@yahoo.com > > Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE > Analysis and DO a BASIC GAGE analysis using those files > > > > Hi Jung, > > > > Thank you for sending your files but there is no need to attach the > > source files from the gage package (GAGE.r, gage.pdf). I have access to > > those files. > > > > The package vignette is just intended to be an example. Clearly the data > > in the package and your data will be very different. It does not make > > sense to try to follow the code exactly "as is" when using your data. > > For example, it doesn't make sense for you to grep for 'HN', 'ADH' and > > 'DCIS' since they don't exist in your file. These are treatment groups > > included in the gage sample data and have no bearing on your analysis. > > This is why you see nothing (i.e., integer(0)) for these variables. > > > > > Micro_array_dataset<- read.table("Micro_array_dataset.txt") > > > cn=colnames(Micro_array_dataset) > > > hn=grep('HN',cn, ignore.case =T) > > > adh=grep('ADH',cn, ignore.case =T) > > > dcis=grep('DCIS',cn, ignore.case =T) > > > print(hn) > > integer(0) > > > print(dcis) > > integer(0) > > > > > > This error is due to the fact that you are subsetting a data.frame and > > have not specified the columns. In the vignette, the gene set is a list > > so this subsetting works. > > > > > lapply(Gene_set[1:3],head) > > Error in [.data.frame(Gene_set, 1:3) : undefined columns selected > > > > > > Next, your genes need to be grouped by pathway. The idea is to do an > > analysis of gene pathways so you need to provide a list of genes grouped > > by pathway (like the kegg.gs or go.gs example files in the vignette). > > Your gene file consists only of gene names, > > > > > head(rownames(Micro_array_dataset)) > > [1] "ENSG00000000003" "ENSG00000000005" "ENSG00000000419" > "ENSG00000000457" > > [5] "ENSG00000000460" "ENSG00000000938" > > > > In R, a list of genes grouped by pathway would look like something like > > this, > > > headkegg.gs) > > $hsa00010 Glycolysis / Gluconeogenesis > > [1] "10327" "124" "125" "126" "127" "128" "130" > > "130589" > > [9] "131" "160287" "1737" "1738" "2023" "2026" "2027" "217" > > ... > > > >$hsa00020 Citrate cycle (TCA cycle) > > [1] "1431" "1737" "1738" "1743" "2271" "283398" "3417" "3418" > > [9] "3419" "3420" "3421" "4190" "4191" "47" "48" "4967" > > ... > > > > You need to identify what pathways you are interested and group the > > genes by those pathways. For identifying pathways take a look at the > > GO.db, KEGG.db or reactome.db. Mapping between gene identifiers can be > > done with the org.*.db packages. > > > > http://www.bioconductor.org/packages/release/data/annotation/ > > > > Some general background on using Bioconductor annotation data is here, > > > > > > > http://www.bioconductor.org/help/workflows/annotation-data /#annotation-resources > > > > > > Valerie > > > > > > On 01/17/12 12:51, Javerjung Sandhu wrote: > >> Hello Valerie, > >> Thanks for your help. I am sending you the data > >> files(Micro_array_dataset.txt**& Gene_Set.txt) which i want to use > >> for the analysis. > >> I need to know in which format the files should be saved (like > >> > http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Da ta_formats > >> this site explains in great detail, what should be the format of the > >> data files required for GSEA analysis (though i am not using GSEA > >> analysis or these file types), same way i want to know in which format > >> i should save the data files required for GAGE analysis so that the > >> analysis is done properly) > >> Please tell me which information is missing from these files. > >> * Yes i know that "gse16873" is expression data and "kegg.gs" is a > >> geneset but i want to use my own, these ones are provided by the author. > >> 1) What i want to accomplish is: I want to do a basic gage analysis > >> (as given in the R script file named "GAGE.r" and pdf file "gage.pdf") > >> such as t-test, rank test, KS test etc. > >> 2) I copied the begining code(to make sure that it loads all the files > >> successfully) from R script file provided by the author (which is also > >> attached as GAGE.r) and made some changes to it and saved as my own > >> script (also attached as Gage_run.r). I tried to load the data files > >> (Micro_array_dataset.txt& Gene_Set.txt) and got these errors (shown > >> in "R Console.txt" file). > >> 3) I run the R script file (Gage_run.r) first to see that it loads all > >> the input files successfully and then i can move ahead with the tests. > >> The output is shown in "R Console.txt" file which shows the errors and > >> warnings. > >> If you need more additional information. Please do tell me. I will be > >> happy to provide that. > >> **an expression matrix with genes as rows and samples as columns. > >> Thanks, > >> Jung > >> ---------------------------------------------------------------- -------- > >> *From:* Valerie Obenchain [vobencha@fhcrc.org] > >> *Sent:* Tuesday, January 17, 2012 10:04 AM > >> *To:* Javerjung Sandhu > >> *Cc:* bioconductor@r-project.org; luo_weijun@yahoo.com > >> *Subject:* Re: [BioC] How to prepare Custom INPUT(DATA) files for GAGE > >> Analysis and DO a BASIC GAGE analysis using those files > >> > >> Hello, > >> > >> I think the vignette is clear that you need (1) a gene set and (2) a > >> mircoarray dataset to run the gage analysis. On page 4 they mention > >> the importance of having the same ID system for your gene set and > >> expression data. Once this is accomplished you can use the gage() > >> function. > >> > >> ## this is the expression data > >> gse16873 > >> > >> ## this is the gene set > >> kegg.gs > >> > >> ## call to gage() using 'HN' as control and 'DCIS' as treatment > >> gse16873.kegg.p<- gage(gse16873, gsets = kegg.gs, > >> ref = hn, samp = dcis) > >> > >> > >> I belive if you have only one column of expression data the 'ref' and > >> 'samp' arguments should be omitted (i.e., default of NULL). Read ?gage > >> for details. Maybe the package author will comment on this. I've cc'd > >> them on this message. > >> > >> It is still not clear to me what you have tried. It would be helpful > >> to know the following, > >> > >> (1) what is your analysis question (what are you trying to accomplish) > >> (2) what have you tried (what functions have you used) > >> (3) what errors have you seen from #2 > >> > >> > >> Valerie > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> On 01/16/2012 04:19 PM, Javerjung Sandhu wrote: > >>> Hi Valerie, > >>> First of all thanks a lot for replying and helping me. I really > appreciate that. I am sending you the R source code file which the GAGE > analysis uses plus two other documents which explains what that package > does. > >>> These are the data files used by the GAGE analysis: > >>> ---------------------------- > >>> Data sets in package gage: > >>> carta.gs Common gene set data collections > >>> egSymb Mapping between Entrez Gene IDs and official > >>> symbols > >>> go.gs Common gene set data collections > >>> gse16873 GSE16873: a breast cancer microarray dataset > >>> kegg.gs Common gene set data collections > >>> ----------------------------------------------------- > >>> I have only ONE tab delimited data file in the form of a MATRIX > giving the gene expressions for 173 patients(as columns) and names of > genes(as rows). > >>> I want to know how can i use this package and my data to do the > GAGE analysis. > >>> If you need more information, please tell me. I will be ready to > provide that. > >>> Thanks, > >>> Jung > >>> > >>> ________________________________________ > >>> From: Valerie Obenchain [vobencha@fhcrc.org] > >>> Sent: Monday, January 16, 2012 3:18 PM > >>> To: Javerjung Sandhu > >>> Cc:bioconductor@r-project.org;luo_weijun@yahoo.com > >>> Subject: Re: [BioC] How to prepare Custom INPUT(DATA) files for > GAGE Analysis and DO a BASIC GAGE analysis using those files > >>> > >>> Hi Jung, > >>> > >>> Please provide the code you've tried and the error you are seeing. For > >>> example, did you read your own data into R, then try to use gage() and > >>> got an error? We can better help you if we understand your inputs and > >>> the function you're having trouble with. > >>> > >>> Valerie > >>> > >>> > >>> On 01/13/12 13:10, Javerjung Sandhu wrote: > >>>> Dear List, > >>>> I will highly appreciate your help on this. > >>>> For the GAGE analysis package shown by the link given below: > >>>> http://www.bioconductor.org/packages/release/bioc/html/gage.html > >>>> Could you please tell me how to prepare the Custom INPUT files > required for this analysis > >>>> OR > >>>> Send me the SAMPLE DATA files in TXT format so that i know in > which format i need to put the data& how could i DO a BASIC GAGE > analysis using those files. I couldn't figure it out and trying it since > 3 weeks or more. > >>>> Best Regards, > >>>> Jung > >>>> > >>>> [[alternative HTML version deleted]] > >>>> > >>>> _______________________________________________ > >>>> Bioconductor mailing list > >>>> Bioconductor@r-project.org > >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>> Search the > archives:http://news.gmane.org/gmane.science.biology.informatics.con ductor > > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 [[alternative HTML version deleted]]