Print Differentially Expressed Exons From Dexseq Results

Question

[justinkablan225]

Hello, I'm trying to do some differential expressed exons analysis with DEXSeq package. I got DEXSeq results by :

dxr1 = DEXSeqResults( dxdEFC, padj>=0.1 )

Then, I'm looking for print only Up-regulate or Down-regulate exons significantly expressed.

Therefore, I done :

write.table(dxr1, "DEXSeq_results" , sep="\t", col.names=T, row.names = T)

This script gave me all genes and exons in a single file within more than 60.000 rows what is very difficult to open and then difficult to sort by padj or FDR.

I think that someone can help me here to resolve that, I will be very grateful.

Best regards.

[justinkablan225]

Dear all,

You don't know how you save me. May GOD bless you more and more.

[justinkablan225]

Hello,

After printing result, I see that some same genes names are listed again in the table with another exonID. Then I've too much genes and exons, that I want is to group same geneID in one wich would group all his exons.

[AK]

Did you mean something like the following?

  groupID     featureID_by_groupID         
1 FBgn0000256 E009,E010,E013      
2 FBgn0000578 E009                
3 FBgn0002921 E012,E015           
4 FBgn0010909 E010                
5 FBgn0020309 E007                
6 FBgn0027579 E001,E002

[justinkablan225]

Yes, exactly that.

[AK]

It can be generated by:

dxr1.sig <- as.data.frame(dxr1[dxr1$padj < 0.1 & !is.na(dxr1$padj),])
library(dplyr)
dxr1.sig.genes <- dxr1.sig %>%
  select(groupID, featureID) %>%
  group_by(groupID) %>%
  mutate(featureID_by_groupID = paste(featureID, collapse = ",")) %>%
  select(-featureID) %>%
  unique()

[justinkablan225]

Hello Thanks lot. It's work perfectly.

[justinkablan225]

Hello, It works but I think somethings wrong looking the results table.

groupID                 exonBaseMean       dispersion      stat             pvalue              padj                    featureID_by_groupID
ENSG00000007202 30.08387115    0.007192981     24.07148254      9.28E-07        0.000566869      E041,E043
ENSG00000007202 5.781795849    0.021773337     12.67383165      0.000370809     0.057097567      E041,E043

The same gene is listed again with different value of dispersion, pvalue and so one. This is an abstract of the results, lot of gene are the same kind of result

I don't inderstand why.

[AK]

Those are different exons as you're testing Differentially Expressed Exons?

[justinkablan225]

I expert that each gene must be listed only one time if it's possible

[lieven.sterck]

Then why are you simply not doing gene expression values in stead of exons? or is this part of the confusion? yes the gene expression is also taking into account the exons but then joined to an mRNA level and thus not keeping them as separate exons

Answer 1

[AK]

Try:

dxr1.sig <- as.data.frame(dxr1[dxr1$padj < 0.1 & !is.na(dxr1$padj),])

then save dxr1.sig using your write.table.

Answer 2

[lieven.sterck]

since you have gotten to the point where you have tab-delineated file with your values, use linux sort or even better awk. Those are applications that allow for easy and powerful manipulation (sorting, filtering on values, ... ) of tab files.