AdjustP=0.05 & gt;
The library (limma) & gt;
Setwd (" C: \ \ Users \ \ RenShuang \ \ Desktop \ \ new folder (3) \ \ 07 diff ") & gt; Rt=read. Table (" normalize. TXT ", sep="\ t", the header=t, check the names=F) & gt;
Rt=as matrix (rt) & gt; Rownames (rt)=rt [1] & gt; Exp=rt [2: ncol (rt)] & gt; Dimnames=list (rownames (exp), colnames (exp)) & gt;
Rt=matrix (as numeric (as matrix (exp)), nrow=nrow (exp), dimnames=dimnames) & gt;
Differential> ModType=c (rep (" normal ", 8), rep (" tumor ", 40), rep (" normal ", 6), rep (" tumor ", 17), rep (" normal ", 15), rep (" tumor ", 31))
The design & lt; - model. Matrix (~ 0 + factor (modType)) & gt; Colnames (design) & lt; - c (" con ", "treat") & gt; Fit & lt; - lmFit (rt, design) & gt; Cont. Matrix<- makeContrasts (treat - con, levels=design)
Fit2 & lt; - contrasts. Fit (fit, cont. Matrix) & gt; Fit2 & lt; - eBayes (fit2) & gt;> AllDiff=topTable (fit2, adjust='FDR', number=200000) & gt; Write. The table (allDiff, file="limmaTab. XLS", sep="\ t", quote=F, row. Names=F) & gt;> # write table> DiffSig & lt; - allDiff [with (allDiff, (abs (logFC) & gt; logFoldChange & amp; adj. P.V al & lt; adjustP)),] & gt; Write. The table (diffSig, file="diff. XLS", sep="\ t", quote=F, row. Names=F)
DiffUp & lt; - allDiff [with (allDiff, (logFC> logFoldChange & amp; adj. P.V al & lt; adjustP)),]
Write. The table (diffUp, file="up. XLS", sep="\ t", quote=F, row. Names=F) & gt; DiffDown & lt; - allDiff [with (allDiff, (logFC<(- logFoldChange) & amp; adj. P.V al & lt; adjustP)),
Write. The table (diffDown, file="the XLS", sep="\ t", quote=F, row. Names=F) & gt;
# write the expression level of diff gene> HmExp=rt [as vector (diffSig [1]),]
The Error in rt [as vector (diffSig [1]),] : subscript out & gt; DiffExp=rbind (id=colnames (hmExp), hmExp)
The Error is in the data frame (x) : can't find the objects' hmExp '& gt; Write. The table (diffExp, file="diffExp. TXT", sep="\ t", quote=F, col. Names=F)
The Error is in the data frame (x) : can't find the objects' diffExp '
What reason be? How to remedy? Thank you for the great god
CodePudding user response:
Check the file before you merge, whether some expression values already took the log and some not, lead to remove the batch effect after the file is wrong,CodePudding user response:
The building Lord, this problem has solvedCodePudding user response:
Do we have to solve the building Lord, I also have the same situation, I looked at my data are taking the log