search for: probeid

Hi, I am using "*Maanova* package" to do anova. I have created *datafile* with probeID as the first column, which is a tab limited text file and also created *designfile*. I have created *readma object* which is named as abf1. >From that readma object, i have to create data object by using *createData*function and also i hav to create model object by using *makemodel* function, th...

I am trying to use lme to fit a mixed effects model to get the same results as when using the following SAS code: proc mixed; class refseqid probeid probeno end; model expression=end logpgc / ddfm=satterth; random probeno probeid / subject=refseqid type=cs; lsmeans end / diff cl; run; There are 3 genes (refseqid) which is the large grouping factor, with 2 probeids nested within each refseqid, and 16 probenos nested within each of the probeids....

Hi all, Im very new to R so please forgive my poor language! I've been trying to map on my list of probeids the relative annotation but unsuccessfully. I get this error symbols <- mget(probes,mouse4302SYMBOL,ifnotfound=NA) Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs Thanks for your help! Brawni -- View this message in context: http://r.789...

Hello, Thanks everyone for helping me with the previous queries. step 1: Here is the orginal data: short sample ProbeID Sample_1_D Sample_1_C Sample_2_D Sample_2_C 1 224588_at 2.425509867 11.34031409 11.46868531 11.75741478 step 2: i calculate the variance of the sample using this R code x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y])#create data.matrix variableprobe<-apply(data...

I am trying to use lme to fit a mixed effects model to get the same results as when using the following SAS code: proc mixed; class refseqid probeid probeno end; model expression=end logpgc / ddfm=satterth; random probeno probeid / subject=refseqid type=cs; lsmeans end / diff cl; run; There are 3 genes (refseqid) which is the large grouping factor, with 2 probeids nested within each refseqid, and 16 probenos nested within each of the probeids....

...ave now forgotten how I did this. So here is my dilemma. I have several thousands of probes (about 180,000) corresponding to each gene; what I'd like to do is obtain is a frequency count of the various occurrences of each probes for each gene. The data would look something like this: Gene ProbeID Expression_Level A 1 0.34 A 2 0.21 E 3 0.11 A 4 0.21 F 5 0.56 F 6 0.87 . . . (180000 data points) In each case, the probeID is uniq...

...eprobe<-apply(data.matrix[x,],1,var) variableprobe #output variance across probesets hist(variableprobe) #displaying histogram of variableprobe write.table(cbind(data[1], Variance=apply(data[,y],1,var)),file='c://variance.csv') #export as a .csv file. Output in Excel all in 1 column. ProbeID "Variance" 1 "224588_at" 21.5825745738848 How do i separate them so that i can have three columns ProbeID Variance 1 224588_at 21.582..... thanks, Kei -- View this message in context: http://www.nabble.com/R-data-Export-to-Excel-tp15796903p15796903.html Sent...

I have a file with a data in columnar format like below: probeID rc_AI104113_at rc_AI178259_f_at rc_AI179134_i_at rc_AI179134_f_at rc_AI104113_at rc_AA819429_f_at How can I rewrite it in the format below: 'rc_AI104113_at', 'rc_AI178259_f_at', 'rc_AI179134_i_at', 'rc_AI179134_f_at', 'rc_AI104113_at', 'rc_AA819429_f_at...

...Thanks for all the help with the previous queries. Here is what i want to do. i have 20000 probesets-->calculate all the variance accross all the probesets-->filter out probesets that are low so now i ended up with only 10000. The 10000 is fine but when i export to excel, it is missing the probeID. Here are my code and examples. #########calculate the variance across the probesets and plot signals######### library(xlsReadWrite) x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y])#create data.matrix variableprobe<-apply(data.matrix[x,],1,var) variableprobe #output variance ac...

Hi, I am using "*Maanova* package" to do anova. I have created *datafile* with probeID as the first column, which is a tab limited text file and also created *designfile*. I have created *readma object* which is named as abf1. >From that readma object, i have to create data object by using *createData*function and also i hav to create model object by using *makemodel* function, th...

...d.madata("rmaexpr.dat",designfile="design.dat") Reading one color array. Otherwise change arrayType='twoColor' then read the data again Warning messages: 1: In read.madata("rmaexpr.dat", designfile = "design.dat") : Assume that the first column is probeid. If you have probeid specify it, otherwise set 'probeid=0' then read the data again 2: In read.madata("rmaexpr.dat", designfile = "design.dat") : Assume that intensity value is saved from the second column. Otherwise provide 'intensity' (first column storing i...

...e", tiffExtGrn="_Grn.TIF", tiffExtRed="_Red.TIF") #################################################### After the above last command (4th one), I got this error message: ****************************************************************** Found 96 arrays Error in order(dat1$ProbeID) : object 'dat1' not found In addition: Warning message: In readIllumina(arrayNames = NULL, useImages = TRUE, singleChannel = FALSE, : No annotation package was specified. Need to use SetAnnotation later ****************************************************************** I will apreciate...

inputfille snpid indid genotype gvariable probeid gene geneexpression rs1040480 CHB_NA18524 C/T 2 GI_19743926-I PTPRT 5.850586 rs1040480 CHB_NA18526 C/C 1 GI_19743926-I PTPRT 6.028641 rs1040480 CHB_NA18529 C/C 3 GI_19743926-I PTPRT 5.944392 rs1040481 CHB_NA18532 C/C 1 GI_19743926-I PTPRT 5.938578 rs1040481 CHB_NA18537 C/C 2 GI_19743926-I PTPRT 5.8...

Hi, I am looking for a solution to boot MY system on any PC. To store most of the system and all of my data I want to use an USB storage (in my case an external USB harddisk (2.0 capable)). Since booting off an USB device is not an universal thing I would prefer to have a boot disk with a minimal system - just enough to load most (all?) of the system from the attached USB device. Is this an

...- would be nice to make PGO/FDO both context-sensitive and flow-sensitive. I think the flow-sensitive part could also integrate with pseudo-probe, essentially we can append FS discriminator later multiple times the same way as you proposed here, except that the "line" part would be "probeId". +Hongtao as well. Thanks, Wenlei From: llvm-dev <llvm-dev-bounces at lists.llvm.org> Date: Tuesday, November 17, 2020 at 9:55 AM To: llvm-dev <llvm-dev at lists.llvm.org> Cc: David Li <davidxl at google.com> Subject: [llvm-dev] [RFC] Control Flow Sensitive AutoFDO (FS-AF...

Hi all, Here I include an RFC for control flow sensitive AutoFDO (FS-AFDO). This is a joint work with David Li. Questions and feedback are welcome. Thanks, Rong ============= [RFC] Control Flow Sensitive AutoFDO (FS-AFDO) 1. Motivation AFDO profile is derived from PMU samples from running an earlier build binary. PMU samples are indexed by the IP addresses. An offline tool uses the debug

...ave now forgotten how I did this. So here is my dilemma. I have several thousands of probes (about 180,000) corresponding to each gene; what I'd like to do is obtain is a frequency count of the various occurrences of each probes for each gene. The data would look something like this: Gene ProbeID Expression_Level A 1 0.34 A 2 0.21 E 3 0.11 A 4 0.21 F 5 0.56 F 6 0.87 . . . (180000 data points) In each case, the probeID is uniq...

...system x86_64, darwin9.8.0 status Patched major 2 minor 11.1 year 2010 month 06 day 03 svn rev 52201 language R version.string R version 2.11.1 Patched (2010-06-03 r52201) THX Assa -------------- next part -------------- ProbeID Transcript ID A_51_P100034 NM_027162.3 A_51_P100052 NM_198863.1 A_51_P100174 NM_008613.2 A_51_P100218 NM_134198.1 A_51_P100227 NM_023579.4 A_51_P100227 NM_023579.4 A_51_P100238 NM_146376.2 A_51_P100298 NM_152220.1 A_51_P100309 NM_001039652.1 A_51_P100327 NM_013683.1 A_51_P100379 NM_17759...