[R] What is the difference between "probe level data" and "summarized data"

Hi all, What is the difference between "probe level data" and "summarized data". Thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/What-is-the-difference-between-probe-level-data-and-summarized-data-tp4639376.html Sent from the R help mailing list archive at Nab

[R] span and epsilon in Cyclic loess

Hi everyone, Is there any automated method to optimize span and epsilon in cyclic loess normalization? I'm using cyclic loess normalization for an array with <1000 genes. Thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/span-and-epsilon-in-Cyclic-loess-tp417191

[R] Bioconductor. MA plot for qPCR array

Dear all, Is there anyway too generate MA plot for 2 qPCR assays (an array of 2x 400). -- View this message in context: http://r.789695.n4.nabble.com/Bioconductor-MA-plot-for-qPCR-array-tp4182805p4182805.html Sent from the R help mailing list archive at Nabble.com.

[R] Binning a 2 column matrix by avarages of rows.

Newbie here. Many apologies in advance for using the incorrect lingo. I'm new to statistics and VERY new to R. I have a "nx2" matrix , I want to sort the values based on the average of 2 columns and put k lowest (or highest) values in bin1, second k high/low values in bin2, and so on (bins would

[R] Smoothing spline with smoothing parameters selected by "generalized maximum likelihood"

Hi there, How may I smooth spline two vectors with the smoothing parameter selected by generalized maximum likelihood (GML) .? Thanks a lot. -- View this message in context: http://r.789695.n4.nabble.com/Smoothing-spline-with-smoothing-parameters-selected-by-generalized-maximum-likelihood-tp4

Re: [R] Bioconductor. MA plot for qPCR array

Dear "Michael Weylandt" and "Juliet Hannah". Thank you indeed very much. -- View this message in context: http://r.789695.n4.nabble.com/Bioconductor-MA-plot-for-qPCR-array-tp4182805p4210685.html Sent from the R help mailing list archive at Nabble.com.

[R] Estimate of smooth.spline

Hi everyone, I have: s= smooth.spline (cbind(1,2,3,4,3,3),cbind (4,2,4,6,5,6)) how may I obtain s hat (s^)? Thanks a lot. -- View this message in context: http://r.789695.n4.nabble.com/Estimate-of-smooth-spline-tp4221253p4221253.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] Estimate of smooth.spline

thank you vey much Jean. On 12/21/11, Jean V Adams [via R] wrote: > > > ali_protocol wrote on 12/21/2011 05:39:19 AM: > >> Hi everyone, >> I have: >> >> s= smooth.spline (cbind(1,2,3,4,3,3),cbind (4,2,4,6,5,6)) >> >> how may I obtain s hat (s^)?

[R] Cumulative distribution of Spearman's Rank rho values.

Hi every one, newbie here. I have a matrix and I want to compute the cumulative distribution of Spearman's Rank rho values, for variables (which are in rows) m= matrix ( rnorm (30), 10,3) how is that done? -- View this message in context: http://r.789695.n4.nabble.com/Cumulative-distributio

[R] How to create a matrix with 3 dimensions from several 2 dimensional matrice?

Hi every one, How is it possible to create a matrix with 3 dimensions from several 2 dimensional matrice? Is it possible that each of "elementary/building block" matrices could be called by its corresponding original name? Thanks alot. -- View this message in context: http://r.789695.n4.n

[R] Cumulative distribution of coefficient of variation.

Hi every one, newbie here. I have a matrix and I want to compute the cumulative distribution of coefficient of variation, for variables (which are in rows) m= matrix ( rnorm (30), 10,3) how is that done? -- View this message in context: http://r.789695.n4.nabble.com/Cumulative-distribution-

[R] ssanova/ ssanova0 and adding the fitted line to a plot.

Hi everyone, I use this code to add the fitted line to a plot, however, I think I cannot access the fitted equation. How my I find the equation in the object ksi? thanks alot. library (gss) generate (simple linear) x and y x= 2* (1:40) y= x-1 plot (x,y) ## fit and draw ksi = ssanova0 (x~y,

[R] What is the function for "smoothing splines with the smoothing parameter selected by generalized maximum likelihood?

Dear all, I am new to R, and I am a biotechnologist, I want to fit a smoothing spline with smoothing parameter selected by generalized maximum likelihood. I was wondering what function implement this, and, if possible how I can find the fitted results for a certain point (or predict from the fit

[R] Creating affybatch objects from matrix (data from qPCR array)

Hi! Is There a way to manually create an affybatch object from qPCR array data? -- View this message in context: http://r.789695.n4.nabble.com/Creating-affybatch-objects-from-matrix-data-from-qPCR-array-tp3921559p3921559.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Creating affybatch objects from matrix (data from qPCR array)

Thanks Martin. Actually I want to do a "cyclic loess", so I chose Affy. How may I find other packages that perform Cyclic loess? -- View this message in context: http://r.789695.n4.nabble.com/Creating-affybatch-objects-from-matrix-data-from-qPCR-array-tp3921559p3927553.html Sent from the R help

[R] How to it a "loess curve" and obtain the equation in R?

Hi! How can I fit a loess curve to an array (384 x 2). How can I obtain the equation for thi fi? Thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/How-to-it-a-loess-curve-and-obtain-the-equation-in-R-tp3927622p3927622.html Sent from the R help mailing list archiv

[R] Changing the size of a plot

Dear all, Newbie. How can I make R create a bigger window for my plot? Thank you in advance. -- View this message in context: http://r.789695.n4.nabble.com/Changing-the-size-of-a-plot-tp4452761p4452761.html Sent from the R help mailing list archive at Nabble.com. ___

[R] Apply a loop containing a function on a list

Hi all, I want to do this: B.list$aa= (a loop containing My.fun acting on the reults of second function on a A.list$aa)) or, overally B.list$aa = function (A.list$aa) B.list and A.list has many sublists aa, ab and Is there a way I can apply the function and

[R] Creat a new list with names of other list

Hi all, I want to create a new list with names of another list. Eeach sublist from both lists is a matrix, but the matrices with the same name (eg. list.1 [[1]] and list.2 [[1]]) have different dimensions. How can I create the 2nd list? tSE = list () Norm <- names(Normal) names(tSE) <- Norm

[R] How to choose the most 2 different samples in an array experiment

Dear all, What test should be done on ~40 samples (matrixes of 400x1), each in triplicate, to determine which sample is the most different to all samples? and What test should be done to determine the two samples which are most different? -- View this message in context: http://r.789695.n4.nab

[R] How to test for the difference of means in population, please help

Dear all, Novice in statistics. I have 2 experimental conditions. Each condition has ~400 points as its response. Each condition is done in 4 repereats (so I have 2 x 400 x 4 points). I want to compare the means of two conditions and test whether they are same or not. Which test should I use?

[R] Testing for difference of distribution of two population(newbie)

Dear all, I am novice in statistics. I have two matrices (results from my experiments), each having ~400 point. I want to test whether the points come from a same distribution or not. Further, I have the results for each matrix (each experiment) in 4 replicates. What should I do? # Repeats of exp

Re: [R] How to test for the difference of means in population, please help

data=obs) > anova(fit) > > > On Mar 27, 3:13 am, ali_protocol > wrote: >> Dear all, >> >> Novice in statistics. >> >> I have 2 experimental conditions. Each condition has ~400 points as its >> response. Each condition is done in 4 repereats (so I have 2

[R] A introductory question about Zips law (Newbie to statistics)

Hi everyone. Newbie to statistics. I have 40 matrices of ~400 values. how may I determine whether the distribution follows zips law? response <-sample (1:20,400*4, replace= TRUE) Thank you vry much. -- View this message in context: http://r.789695.n4.nabble.com/A-introductory-question-about-

[R] Sum of sd between matrix cols vs spearman correlation between them

Hi all, I have a matrix (n*2), I want to compare 2 operators (2 normalization for array results) on these matrix. The 2 columns should ideally become the same after operations (normalization). So to compare operations, I do this for each normalization: s= sum (apply (normalized.matrix, 2,sd))

Re: [R] Sum of sd between matrix cols vs spearman correlation between them

e: > > > On Thu, Apr 05, 2012 at 07:46:52AM -0700, ali_protocol wrote: >> Hi all, >> >> I have a matrix (n*2), I want to compare 2 operators (2 normalization for >> array results) on these matrix. >> The 2 columns should ideally become the same after operations

[R] Comparing 2 means. pls help

I am interested in the difference of 2 data: mat1= c(2.2, 2.3, 2.2,2.5) mat2= c(2.6, 2.8, 2.7,2.4) mat= mat2-mat1 I perform an action on both mat1 and mat2, and I get mat1prime and mat2prime: mat1prime= c(2.5, 2.5, 2.3,2.5) mat2prime= c(2.6, 2.8, 2.7,2.6) matprime= mat2prime-mat1prime I want

[R] What is the fastest way to combine all columns of a matrix to one column?

Dear all, Newbie: What is the fastest way to combine all columns of a matrix to one column? -- View this message in context: http://r.789695.n4.nabble.com/What-is-the-fastest-way-to-combine-all-columns-of-a-matrix-to-one-column-tp4423882p4423882.html Sent from the R help mailing list archive at

[R] Obtaining translated, rotated and scaled matrics in procrustes analysis

Hi all, I wondered how I can get the translated, rotated and scaledmatrix in a procrustes analysis. This does not help: ## library (vegan) #defining the target matrix: a= cbind (c (1,2,3,4), c( 10,12,14,16)) #defining the matrix to be rotated: b= a; b[,2]= c(9,11,15,

[R] Weired location of points on MA plot?

Dear all, I have a MA plot for "replicate" single channnel arrays, the loess curve is aligned to M=0. However, I expect that M values be as close as possible to M=0 for replicate arrays, which is not the case. How may I obtain a measure that indicates the average distance of points to M=0? Than