Checking output of DESeq package analysis
1
0
Entering edit mode
Guest User ★ 13k
@guest-user-4897
Last seen 9.6 years ago
I run DESeq package on my RNA seq hit count data (without replication). The input (hit count values) and output values (base means A & B) in the columns are the same. I want to make sure that these results are reliable as with a dataset of 78774 rows all the input values are the same as output values. I am getting fold changes and p-values which seems to be correct. The code and outputs are given below: (My code is running fine, my concern is output values (base mean A and B ) which are the same as WT_hit_counts and Mutant_hit_counts)values. I think for some reason code is returning right p values but not the right base means. I will appreciate your help. -- output of sessionInfo(): > countsTable <- read.delim("filepath.txt", header=TRUE, stringsAsFactors=FALSE,row.names=1) > conds <- factor(c("X", "Y")) > head(countsTable) WT_hit_counts Mutant_hit_counts Gene 1 1 6 Gene 2 9 13 Gene 3 10 34 Gene 4 34 20 Gene 5 2 2 Gene 6 8 18 > cds3 <- newCountDataSet( countsTable, conds ) > cds3 <- estimateSizeFactors( cds3 ) > cds3 <- estimateDispersions( cds3, method="blind",sharingMode="fit- only") > res <- nbinomTest(cds3,"X","Y") > head(res) id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj Gene 1 3.5 1 6 6.00 2.58 0.754 1 Gene 2 11.0 9 13 1.44 0.530 0.883 1 Gene 3 22.0 10 34 3.40 1.76 0.381 1 Gene 4 27.0 34 20 0.588 -0.76 0.67 1 Gene 5 2.0 2 2 1.00 0.00 1.00 1 Gene 6 13.0 8 18 2.25 1.16 0.67 1 -- Sent via the guest posting facility at bioconductor.org.
DESeq DESeq • 636 views
ADD COMMENT
0
Entering edit mode
Simon Anders ★ 3.7k
@simon-anders-3855
Last seen 3.7 years ago
Zentrum für Molekularbiologie, Universi…
Hi On 2012-04-09 22:58, Anupreet kour [guest] wrote: > > I run DESeq package on my RNA seq hit count data (without > replication). The input (hit count values) and output values (base > means A& B) in the columns are the same. I want to make sure that > these results are reliable as with a dataset of 78774 rows all the > input values are the same as output values. I am getting fold changes > and p-values which seems to be correct. The code and outputs are > given below: (My code is running fine, my concern is output values > (base mean A and B ) which are the same as WT_hit_counts and > Mutant_hit_counts)values. I think for some reason code is returning > right p values but not the right base means. I will appreciate your > help. The baseMeans are simply the genewise means of the normalized counts. If you have only one sample per condition, it is hence the normalized count itself. In you case, the normalization seems to have had no effect -- your sizeFactors seem to be 1. This may happen if you have very low count values. In this case, using the shorth (see ?estimateSizeFactors) might work better. In the end, however, with as low count values and no proper replication, I am afraid it is unlikely that fixing the normalization will help much in getting a signal from your data. Simon
ADD COMMENT

Login before adding your answer.

Traffic: 904 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6