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...s the coding for volcano plot, i hope anybody can help me to solve the problem. #    volcano_plot.r # #    Author:    Amsha Nahid, Jairus Bowne, Gerard Murray #    Purpose:    Produces a volcano plot # #    Input:    Data matrix as specified in Data-matrix-format.pdf #    Output:    Plots log2(fold change) vs log10(t-test P-value) # #    Notes:    Group value for control must be alphanumerically first #              Script will return an error if there are more than 2 groups # #    Load the data matrix # # Read in the .csv file data<-read.csv("file:///Users/nadya/Desktop/praktikal UT...

...rray field in a Postgresql database. Here is the table definition. View "neil.flashing_codes" Column | Type | Modifiers -------------+-----------------------+----------- code | character varying(10) | description | text | folds | integer[] | View definition: SELECT flashings.code, max(flashings.description::text) AS description, array_accum(flashings.folds) AS folds FROM flashings GROUP BY flashings.code; Here is a sample of the records. select * from flashing_codes limit 10; code |...

Hi Duncan, Thank you a lot for your time to provide that great and informative explanation. Now the "undef" logic makes much more sense for me. >> /You are wrong to say that "div undef, %X" is folded to "undef" by InstructionSimplify, it is folded to zero./ My mistake. I meant to say "*f****div* undef, %X" is folded to "undef" (not integer "div"). >> /Fdiv is harder than div because a floating point division by 0.0 has a defined result, unlik...

...ow coding for volcano. what is the mistake? what the plot could not display? # volcano_plot.r # # Author: Amsha Nahid, Jairus Bowne, Gerard Murray # Purpose: Produces a volcano plot # # Input: Data matrix as specified in Data-matrix-format.pdf # Output: Plots log2(fold change) vs log10(t-test P-value) # # Notes: Group value for control must be alphanumerically first # Script will return an error if there are more than 2 groups # # Load the data matrix # # Read in the .csv file data<-read.csv("input5.csv", sep=",", row...

.../llvm.org/docs/LangRef.html#undefined-values However, those examples do not cover all of the possible contexts where /"undef"/ can appear. E.g., I can't realize why /"fmul undef, undef"/ may not result in/"undef"/ whereas /"mul undef, undef"/ is always folded to /"undef"/. Seems I am missing something important about floats here. The same applies to "fdiv". /"fdiv undef, undef"/ is not folded but /"div %X, undef"/ and /"div undef, %X"/ are folded to /"undef"/ (SimplifyFDivInst function in...

...n %bb.1 with a mov instruction. As we move such spill down to its successor, we can also encourage more shrink-wrapping as well. .globl _mytest // %bb.0: // %entry sub sp, sp, #224 // =224 stp x28, x27, [sp, #128] // 8-byte Folded Spill stp x26, x25, [sp, #144] // 8-byte Folded Spill stp x24, x23, [sp, #160] // 8-byte Folded Spill stp x22, x21, [sp, #176] // 8-byte Folded Spill stp x20, x19, [sp, #192] // 8-byte Folded Spill stp x29, x30, [sp, #20...

...ant to use the data set from this loop to plot curves. I have tried return, list, but I can not use the *tree.pred* data and *valid.out* vector. auc.tree<- function(msplit,mbucket) { * tree.pred<-data.frame() valid.out<-vector()* for(i in 1:10) { cat('Fold ', i, '\n') out.fold.c <-((i-1)*c.each.part +1):(i*c.each.part) out.fold.n <-((i-1)*n.each.part +1):(i*n.each.part) train.cv <- n.cc[-out.fold.c, c(2:401, 418)] train.nv <- n.nn[-out.fold.n, c(2:401, 418)] train.v<-rbind(train.cv, tra...

...attern of an snan, > for some other fdiv optimization the compiler can choose it to be 1.0 > if that is convenient. > >> The question is whether we can make the same assumption for other >> floating point >> operations, or "fdiv" needs a correction to prevent folding since >> signalling of >> SNaNs might be disabled. > > You can assume that undef is an snan if you want in any floating point > operation. But what does that assumption buy you? If you are willing > to assume that the processor will trap on snans then it buys you a l...

All, The CentOS Folding at Home team has cracked the top 10% of all the folding teams. We could use some more members that have CPU Cycles to spare :) Folding at Home is a great distributed computing program that is used to process items for medical research teams. It is similar to SETI at Home (if you are familiar...

...such spill down to > its successor, we can also encourage more shrink-wrapping as well. > > .globl _mytest > > // %bb.0: // %entry > > sub sp, sp, #224 // =224 > > stp x28, x27, [sp, #128] // 8-byte Folded Spill > > stp x26, x25, [sp, #144] // 8-byte Folded Spill > > stp x24, x23, [sp, #160] // 8-byte Folded Spill > > stp x22, x21, [sp, #176] // 8-byte Folded Spill > > stp x20, x19, [sp, #192] // 8-byte Folded S...

Hi Duncan, On 17.09.2014 21:10, Duncan Sands wrote: > Hi Oleg, > > On 17/09/14 18:45, Oleg Ranevskyy wrote: >> Hi, >> >> Thank you for all your helpful comments. >> >> To sum up, below is the list of correct folding examples for fadd: >> (1) fadd %x, -0.0 -> %x >> (2) fadd undef, undef -> undef >> (3) fadd %x, undef -> NaN (undef is a NaN which >> is propagated) >> >> Looking through the code I found...

cv.fold<-function(i, size=3, rang=0.3){ cat('Fold ', i, '\n') out.fold.c <-((i-1)*c.each.part +1):(i*c.each.part) out.fold.n <-((i-1)*n.each.part +1):(i*n.each.part) train.cv <- n.cc[-out.fold.c, c(2:2401, 2417)] train.nv <- n.nn[-out.fold.n...

Hi, Thank you for all your helpful comments. To sum up, below is the list of correct folding examples for fadd: (1) fadd %x, -0.0 -> %x (2) fadd undef, undef -> undef (3) fadd %x, undef -> NaN (undef is a NaN which is propagated) Looking through the code I found the "NoNaNs" flag accessed through an inst...

...n %bb.1 with a mov instruction. As we move such spill down to its successor, we can also encourage more shrink-wrapping as well. .globl _mytest // %bb.0: // %entry sub sp, sp, #224 // =224 stp x28, x27, [sp, #128] // 8-byte Folded Spill stp x26, x25, [sp, #144] // 8-byte Folded Spill stp x24, x23, [sp, #160] // 8-byte Folded Spill stp x22, x21, [sp, #176] // 8-byte Folded Spill stp x20, x19, [sp, #192] // 8-byte Folded Spill stp x29, x30, [sp, #20...

Hello! I have a question. I am working with createFolds: folds<- trainControl(method='cv', index=createFolds(data$Score,list = TRUE)) I need to iterate over folds to extract the indexes from each fold. For example, if I do folds$index$Fold01, it contains: 5 11 17 29 44 50 52 64 65 I need to iterate over each $Fold_i to extract the...

I am new to R and have two scripts written slightly different but should to relatively the same thing but my lack of experience with the program I can not figure out the what I need to do to correct it. The first script gives me a consistent mean fold change values with every run but can generate negative p values for some. For the second version of the script, the fold changes seem to be very random but the p values do not go negative. I have highlighted the differences in the script that I noticed. I am think some combination of these two...

...or, we can also encourage more shrink-wrapping as well. > > > > .globl _mytest > > > > // %bb.0: // %entry > > > > sub sp, sp, #224 // =224 > > > > stp x28, x27, [sp, #128] // 8-byte Folded Spill > > > > stp x26, x25, [sp, #144] // 8-byte Folded Spill > > > > stp x24, x23, [sp, #160] // 8-byte Folded Spill > > > > stp x22, x21, [sp, #176] // 8-byte Folded Spill > > > > stp x20, x...

..., Duncan Sands <duncan.sands at deepbluecap.com> wrote: > > I think you should try to get LLVM floating point experts involved, to find out their opinion about whether LLVM should really assume that snans always trap. > > If they think it is fine to assume trapping, then you can fold any floating point operation with an "undef" operand to "undef". > > If they think it is no good, then the existing folds that use this need to be removed or weakened, though maybe another argument can be found to justify them. LLVM is used to target many platforms for w...

As far as I know, LLVM does not try very hard to guarantee constant folded NaN payloads that match exactly what the target would generate. —Owen > On Sep 16, 2014, at 10:30 AM, Oleg Ranevskyy <llvm.mail.list at gmail.com> wrote: > > Hi Duncan, > > I reread everything we've discussed so far and would like to pay closer attention to the the AR...

...t; representable in the destination format"./ thanks for finding this out. > > Floating point add propagates a NaN. There is no conversion in the context of > LLVM's fadd. So, if %x in "fadd %x, -0.0" is a NaN, the result is also a NaN > with the same payload. Yes, folding "fadd %x, -0.0" to "%x" is correct. This implies that "fadd undef, undef" can be folded to "undef". > > As regards "fadd %x, undef", where %x might be a NaN and undef might be chosen > to be (probably some different) NaN, and a possib...