Question: Breast cancer TCGA data - DGE analysis
gravatar for David_emir
4.0 years ago by
David_emir330 wrote:

Hello All,

I am applying Voom normalization to RNA-Seq raw Counts data obtained from TCGA. I have constructed a Matrix of ~20000 Rows and 341 Coloumns with first column being of Gene_id.

I am using Voom() method to normalise the data. I have done the following code.

## Librarys

## Matrix File <-read.delim("Combined_matrix_340.txt")
d <-[, 2:341]
rownames(d) <-[, 1]

# Pheno data file
pheno<-read.table("pheno_data_BRCA.txt", header=TRUE, sep="\t")

##To design matrix---

y <- voom(d,design,plot=TRUE)


fit <-lmFit(y,design)

##Designing Contrast Matrix for group Differentiation


fit2 <,cont.wt)

DE<-topTable(fit3, coef=2 )

After This, The out put is as follows:

 Gene_ID        logFC       AveExpr        t              P.Value            adj.P.Val        B
ACTB|60       12.59366   12.54151     202.8138  0.000000e+00  0.000000e+00 806.7855
EEF1A1|1915   12.06986 12.51399 187.5779  0.000000e+00  0.000000e+00 781.7838
ACTG1|71      11.93940 12.03115 179.5847  0.000000e+00  0.000000e+00 767.7521
UBC|7316      10.71139 11.15274 176.8877  0.000000e+00  0.000000e+00 761.7751
TPT1|7178     10.99882 11.58788 159.5321  0.000000e+00  0.000000e+00 728.9007
HSP90AB1|3326 11.00446 11.12925 157.1734 9.881313e-323 3.381237e-319 724.0502
FTH1|2495     10.98239 11.26717 153.0514 8.557019e-319 2.509774e-315 715.3888
EEF2|1938     10.82150 11.46502 151.3403 3.886332e-317 9.973786e-314 711.5412
PSAP|5660     10.71044 11.06326 147.8964 9.572234e-314 2.183639e-310 703.8942
HSP90AA1|3320 10.74747 10.94257 144.5401 2.294330e-310 4.710489e-307 696.4700

My Question: I am Getting only a list of 10 genes, i am not able to pull all list. And, I want someone to validate my codes and method followed. Let me remind you all, i am a novice in coding/Bioinformatics. Please let me know if i am coding it correct or should i modify it.

Thanks a lot for your help.

-Ateeq Khaliq



voom rna-seq tcga raw_count • 1.5k views
ADD COMMENTlink written 4.0 years ago by David_emir330
DE = topTable(fit3, coef = 2, number = 'all')

gives all genes. Default topTable outputs only top ten genes.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by poisonAlien2.8k

Thanks a lot poisonAlien.... Can you please Validate my code ? 

ADD REPLYlink written 4.0 years ago by David_emir330

David, Could you please help me and tell me how did you construct the matrix?

ADD REPLYlink written 3.1 years ago by hAjmal30
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