Displaying 7 results from an estimated 7 matches for "logfc".
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logfp
2010 Jan 31
2
Using apply function on duplicates in a data.frame
...pSysX_49 pSysX_49
4042 3843 0 pSysX_51_18_1 pSysX_51 pSysX_51
3646 3466 0 sll1514_0_2 sll1514 sll1514
2946 2807 0 sll1514_0_1 sll1514 sll1514
624 582 0 pSysX_49_8_2 pSysX_49 pSysX_49
Description logFC AveExpr t P.Value adj.P.Val
1665 Unknown 4.3887 9.5662 61.038 1.0938e-08 9.4449e-05
5422 Unknown -3.5251 6.9103 -35.908 1.7596e-07 3.5912e-04
4042 Unknown 2.5302 8.7497 35.112 1.9786e-07 3.5912e-04
3646 Unknown 2.3457 11.1678 33.962 2.3549e-07 3.5912e-04
2946...
2012 Jun 12
1
Analyzing large files faster
I'm trying to analyze the following data set (sample):
"ID" "adj.P.Val" "logFC" "Gene.symbol"
"1419156_at" "5.32e-12" "2.6462565" "Sox4"
"1433575_at" "5.32e-12" "3.9417089" "Sox4"
"1428942_at" "2.64e-11" "3.9163618" "Mt2"
"1454699_...
2008 Feb 11
3
Difference between P.Value and adj.P.Value
Hallo,
> fit12<-lmFit(qrg[,1:2])
> t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1])
> t12
ID logFC t P.Value adj.P.Val B
522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965
1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046
Can anyone tell me what the difference is between P.Value and
adj.P.Value? I need to analyse microarrays and should say...
2012 Nov 17
1
fold change calculation
Hi,
I am really new to edge R and I have used it to calculate gene expression
with RNASeq data comparing 2 different conditions.
I used a P value of 0.05 and I got a list of DGE contigs up and down
regulated.
WhatI was wondering is how to convert the logFC value that appear in the
output of the exact test.
Is it a log2 base? Is fold 2 change considered as cutoff?
I am trying to find this info on the manual but apparently I am not able.
Could someone help me?
Thanks so much
Vittoria
--
Vittoria Roncalli
Graduate Research Assistant
Center Békésy...
2008 Jan 24
3
store variable as tab-del. txt-file
Hallo,
how can I store a variable as a tab-delimited txt-file? I crated a
variable with the following commands:
> fit12<-lmFit(qrg[,1:2])
> t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1])
> t12
ID logFC t P.Value adj.P.Val B
522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965
1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046
767 CD44_WIZ -8.164317 -8.201678 6.648556e-05 0.01212520 1.928622
1234 EMP1_WIZ -6.822609 -8.145985 6.953146e-05 0.01...
2008 Nov 23
4
help needed
hi I have a matrix (10x10) and I have to perform t tests on each row by
considering first 5 elements as data set A and next 5 as data set B. This
part is easy, However after one t test on each row, I have to randomly
permute each column to get new values for each row and then perform another
t.test. I can permute the column randomly using the function sample(x) but i
am having problem in fitting
2011 Feb 09
1
samr - extract genes from siggenes.table
Hi BioC user,
I have a problem extracting the gene set I would like to work with.
Here is I work with my data:
normData <- read.delim("normalizedData.txt",sep ="\t")
######### two class unpaired comparison
# y must take values 1,2
classes <- c(-1,-2,1,2)
#prepere the data for the samr analysis
data.x <-as.matrix(normData[,8:11])
d=list(x=data.x,y=classes,