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Dear meta-analysis users, I have collected raw data from five observational studies, so a total of 1300 observations or patients, then for each patients there are 17,000 variables, since all five studies used the same method to measure...

HI Bert, Thank you for extra help!! Yes, exactly, your interpretation is perfectly correct and your R code is what I should look for. after generated all those negative values of correlation, I thought about the extremely small p values...

Hi R users, I generated a square correlation matrix for the dat dataframe below; dat<-data.frame(g1=c(1,0,0,1,1,1,0,0,0), g2=c(0,1,0,1,0,1,1,0,0), g3...

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...

sorry, this is not a homework question although I am working at home now due to COVID19 virus spreading in California. I tried to write a function to convert input data file. > tem4$Var1 [1] 1 3 4 5 6...

Hi Deepayan, Thank you very much!! Yes, your method also works very well, I thought about creating an extra time variable, but did not know how to do it. Ding ________________________________________ From: Deepayan Sarkar [deepayan.sarkar at gmail.com] Sent: Saturday...

Hi Wolfgang, Thank you so much for your help!!! I got it. Yuan Ding ________________________________________ From: Viechtbauer, Wolfgang (SP) [wolfgang.viechtbauer at maastrichtuniversity.nl] Sent: Thursday, July 18, 2019 4:46 AM To: Yuan Chun Ding; r-sig-meta-analysis at...

You **might** do better pursuing this sort of thing on the Bioconductor site: https://www.bioconductor.org/help/<https://urldefense.com/v3/__https://www.bioconductor.org/help/__;!!Fou38LsQmgU!441uqddHFvpuq6wfAy-jNNUZ8Dz_jGxN9itKerhoPxav-yjaqUkpwPhN4bJJ$> They often have professionally written R packages tailored...

sorry, I just came back. Yes, Abby's understanding is right. > tem4$Var1 [1] 1 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 25 31 > tem4$Freq...

after add intercept, all residuals are the same from lm or lm.fit. Ding From: Bert Gunter <bgunter.4567 at gmail.com> Sent: Saturday, August 10, 2024 1:00 PM To: Yuan Chun Ding <ycding at coh.org> Cc: Ben...

Hi Bert and Ben, Thanks a lot for your suggestion!!. About the different residuals between lm function and lm.fit, from online search, lt seems like that I need to add an intercept in the design matrix x; pur2 <- matrix...

Hi Bert, Thank you for the elegant code example. I achieved my goal using lapply function and do.call function together. Reduce function is nicer one and I am looking into it. Ding From: Bert Gunter [mailto:bgunter.4567 at...

Hi Bert, your code worked perfect. you always make me learn new R code skills! Thank you so much!! Ding ________________________________________ From: Bert Gunter [bgunter.4567 at gmail.com] Sent: Tuesday, April 7, 2020 12:53 PM To: Yuan Chun Ding...

Dear R users, I have a numeric table with 140 rows and 30 columns, here I only made partial table, test1, as an example. I want to apply a blue color range to the value in each cell of the...

Hi Rui, You are always very helpful!! Thank you, I just modified your R codes to remove a row with zero values in both column pair as below for my real data. Ding dat<-gene22mut.coded r <- P <- matrix(NA...

HI Rui, Thank you for the help! You did not remove a row if zero values exist in both column pair, right? Ding From: Rui Barradas <ruipbarradas at sapo.pt> Sent: Thursday, July 25, 2024 11:15 AM To: Yuan...

I am sorry that I know I should provide a dataset that allows to replicate my problem. It is a research dataset and quite large, so I can not share. Both Bert and Tim guessed my problem correctly. I also...

Hi Jim, Thank you so much for your help! I looked into the plotrix package, the addtable2plot function can do somewhat I want by creating an empty plot first. Ding -----Original Message----- From: Jim Lemon [mailto:drjimlemon at gmail.com...