[R] a fast way to do my job

Yuan Chun Ding ycd|ng @end|ng |rom coh@org
Sat Aug 10 22:08:47 CEST 2024 

You are right.  I also just thought about that, no intercept is not applicable to my case.

Ding

From: Bert Gunter <bgunter.4567 using gmail.com>
Sent: Saturday, August 10, 2024 1:06 PM
To: Yuan Chun Ding <ycding using coh.org>
Cc: Ben Bolker <bbolker using gmail.com>; r-help using r-project.org
Subject: Re: [R] a fast way to do my job

Ah, messages crossed. A no-intercept model **assumes** the straight line fit must pass through the origin. Unless there is a strong justification for such an assumption, you should include an intercept. -- Bert On Sat, Aug 10, 2024 at 1: 02 PM


Ah, messages crossed.

A no-intercept model **assumes** the straight line fit must pass

through the origin. Unless there is a strong justification for such an

assumption, you should include an intercept.



-- Bert



On Sat, Aug 10, 2024 at 1:02 PM Bert Gunter <bgunter.4567 using gmail.com<mailto:bgunter.4567 using gmail.com>> wrote:

>

> Is it because I failed to to add a column of ones for an intercept to

> the x matrix? TRhat would be my bad.

>

> -- Bert

>

>

> On Sat, Aug 10, 2024 at 12:59 PM Bert Gunter <bgunter.4567 using gmail.com<mailto:bgunter.4567 using gmail.com>> wrote:

> >

> > Probably because you inadvertently ran different models. Without your code, I haven't a clue.

> >

> >

> > On Sat, Aug 10, 2024, 12:29 Yuan Chun Ding <ycding using coh.org<mailto:ycding using coh.org>> wrote:

> >>

> >> HI Bert and Ben,

> >>

> >>

> >>

> >> Yes, running lm.fit using the matrix format is much faster. I read a couple of online comments why it is faster.

> >>

> >>

> >>

> >> However, the residual values for three tested variables or genes from lm function and lm.fit function are different, with Pearson correlation of 0.55, 0.89, and 0.99.

> >>

> >>

> >>

> >> I have not found the reason.

> >>

> >>

> >>

> >> Thanks,

> >>

> >>

> >> Ding

> >>

> >>

> >>

> >> From: Bert Gunter <bgunter.4567 using gmail.com<mailto:bgunter.4567 using gmail.com>>

> >> Sent: Friday, August 9, 2024 7:11 PM

> >> To: Ben Bolker <bbolker using gmail.com<mailto:bbolker using gmail.com>>

> >> Cc: Yuan Chun Ding <ycding using coh.org<mailto:ycding using coh.org>>; r-help using r-project.org<mailto:r-help using r-project.org>

> >> Subject: Re: [R] a fast way to do my job

> >>

> >>

> >>

> >> Better idea, Ben! It would work as you might expect it to to produce the same results as the above: ##first make sure your regressor is a matrix: pur2 <- matrix(purity2, ncol =1) ## convert the data frame variables into a matrix dat <-

> >>

> >> Better idea, Ben!

> >>

> >>

> >>

> >> It would work as you might expect it to to produce the same results as

> >>

> >> the above:

> >>

> >>

> >>

> >> ##first make sure your regressor is a matrix:

> >>

> >> pur2 <- matrix(purity2, ncol =1)

> >>

> >> ## convert the data frame variables into a matrix

> >>

> >> dat <- as.matrix(gem751be.rpkm[ , 74:35164])

> >>

> >> ##then

> >>

> >> result <- residuals(lm.fit( x= pur2, y = dat))

> >>

> >>

> >>

> >> Cheers,

> >>

> >> Bert

> >>

> >>

> >>

> >> On Fri, Aug 9, 2024 at 6:38 PM Ben Bolker <bbolker using gmail.com<mailto:bbolker using gmail.com>> wrote:

> >>

> >> >

> >>

> >> > You can also fit a linear model with a matrix-valued response

> >>

> >> > variable, which should be even faster (not sure off the top of my head

> >>

> >> > how to get the residuals and reshape them to the dimensions you want)

> >>

> >> >

> >>

> >> > On Fri, Aug 9, 2024 at 9:31 PM Bert Gunter <bgunter.4567 using gmail.com<mailto:bgunter.4567 using gmail.com>> wrote:

> >>

> >> > >

> >>

> >> > > See ?lm.fit.

> >>

> >> > > I must be missing something, because:

> >>

> >> > >

> >>

> >> > > results <- sapply(74:35164, \(i) residuals(lm.fit(purity2,

> >>

> >> > > gem751be.rpkm[, i] )))

> >>

> >> > >

> >>

> >> > > would give you a 751 x 35091 matrix of the residuals from each of the

> >>

> >> > > regressions.

> >>

> >> > > I assume it will be considerably faster than all the overhead you are

> >>

> >> > > carrying in your current code, but of course you'll have to try it and

> >>

> >> > > see. ... Assuming that I have interpreted your request correctly.

> >>

> >> > > Ignore if not.

> >>

> >> > >

> >>

> >> > > Cheers,

> >>

> >> > > Bert

> >>

> >> > >

> >>

> >> > > On Fri, Aug 9, 2024 at 4:50 PM Yuan Chun Ding via R-help

> >>

> >> > > <r-help using r-project.org<mailto:r-help using r-project.org>> wrote:

> >>

> >> > > >

> >>

> >> > > > Dear R users,

> >>

> >> > > >

> >>

> >> > > > I am running the following code below,  the gem751be.rpkm is a dataframe with dim of 751 samples by 35164 variables,  73 phenotypic variables in the furst to 73rd column and 35091 genomic variables or genes in the 74th to 35164th columns.  What I need to do is to calculate the residuals for each gene using the simple linear regression model of genelist[i] ~ purity2;

> >>

> >> > > >

> >>

> >> > > > The following code is running,  it takes long time, but I have an expensive ThinkStation window computer.

> >>

> >> > > > Can you provide a fast way to do it?

> >>

> >> > > >

> >>

> >> > > > Thank you,

> >>

> >> > > >

> >>

> >> > > > Ding

> >>

> >> > > >

> >>

> >> > > > ---------------------------------------------------------------------------------

> >>

> >> > > >

> >>

> >> > > >

> >>

> >> > > > gem751be.rpkm <-merge(gem751be10, as.data.frame(t(rna849.fpkm2)),

> >>

> >> > > > +                           by.x="id2",by.y=0)

> >>

> >> > > > >   row.names(gem751be.rpkm)<-gem751be.rpkm$id3

> >>

> >> > > > >   colnames(gem751be.rpkm)<-gsub(colnames(gem751be.rpkm),pattern="-",replacement="_")

> >>

> >> > > > >   genelist <- gem751be.rpkm %>% dplyr::select(74:35164)

> >>

> >> > > > >   residuals <- NULL

> >>

> >> > > > >   for (i in 1:length(genelist)) {

> >>

> >> > > > +     #i=1

> >>

> >> > > > +     formula <- reformulate("purity2", response=names(genelist)[i])

> >>

> >> > > > +     model <- lm(formula, data = gem751be.rpkm)

> >>

> >> > > > +     resi <- as.data.frame(residuals(model))

> >>

> >> > > > +     colnames(resi)[1]<-names(genelist)[i]

> >>

> >> > > > +     resi <-as.data.frame(t(resi))

> >>

> >> > > > +     residuals <- rbind(residuals, resi)

> >>

> >> > > > +   }

> >>

> >> > > >

> >>

> >> > > >

> >>

> >> > > >

> >>

> >> > > > ----------------------------------------------------------------------

> >>

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> >>

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> >>

> >> > >

> >>

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