Displaying 20 results from an estimated 80 matches similar to: "fold change calculation"
2011 Nov 07
1
DESeq
Hello,
I have RNAseq data, which I am trying to analyze with DESeq. My file (tab delimited .txt) appears to be correct:
>head(myfile)
VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a
ENSG00000253101 0 0 0 0 0 0
ENSG00000223972 0 0 0 0 0 0...
However, when I try to analyze the data with
>cds <-
2010 Aug 05
2
colour of label points on a boxplot
Hi all,
I have 6 datasets(dataframes Assem_ContigsLen7 through all_ContigsLen12)
containing 3 columns (contig_id, contig_length, read_count).
Each dataset is composed of 3 types of contigs (assemblies of genomic
fragments), 1- all Bacterial fragments, 2 - all Viral fragments, 3 -
mixed fragments.
I identified the type of contig through a merge with another table with
just contig_id and
2010 Feb 02
2
using rbind in a for loop
*Dear R users,
*I'm facing a trivial problem but I cannot solve it.
My question is:
I want to make data set like this.
>
i_lon1 i_lat1
i_lon2 i_lat2
i_lon3 i_lat3
i_lon4 i_lat4
>
i+1_lon1 i+1_lat1
i+1_lon2 i+1_lat2
i+1_lon3 i+1_lat3
i+1_lon4 i+1_lat4
>
i+2_lon1 i+2_lat1
i+2_lon2 i+2_lat2
i+2_lon3 i+2_lat3
i+2_lon4 i+2_lat4
.
.
.
>
i+5_lon1 i+5_lat1
i+5_lon2 i+5_lat2
i+5_lon3
2010 Jan 31
2
Using apply function on duplicates in a data.frame
Dear R-Helpers,
I have a data.frame (df) and the head of data.frame looks like
ProbeUID ControlType ProbeName GeneName SystematicName
1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50
5422 5147 0 pSysX_49_8_1 pSysX_49 pSysX_49
4042 3843 0 pSysX_51_18_1 pSysX_51 pSysX_51
3646 3466 0 sll1514_0_2 sll1514 sll1514
2017 Jun 09
2
Dendogram from RNAseq read count to show correlation between biological replicate using R
Dear all,
I need to make dendogram from read count in a csv file across 34 samples
including biological replicate.
Please share R code or package to do this.
Do I also need to normalized read count before using read data?
Thanks
[[alternative HTML version deleted]]
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"
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$genes[,1])
> t12
ID logFC t P.Value adj.P.Val B
522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965
1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046
Can anyone tell me what the difference is between P.Value
2008 Jan 24
3
store variable as tab-del. txt-file
Hallo,
how can I store a variable as a tab-delimited txt-file? I crated a
variable with the following commands:
> fit12<-lmFit(qrg[,1:2])
> t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$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
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,
2004 Dec 17
5
Total newbie here looking to do a VoIP conference call?
I am looking to help out my company find a more budget conscious but
reliable way to hold conference calls between 5+ people. 4x a month we hold
several hour long conference calls during non-business hours. All of the
employees have high speed internet. Currently we dial up an AT&T conf using
regular analog phones.
I don't have a great grasp as to what Asterick is capable of, but my
2009 Oct 29
5
Summing identical IDs
Hello All,
I would like to select records with identical IDs then sum an attribute
then and return them to the data frame as a single record. Please consider
Acres<-c(100,101,100,130,156,.5,293,300,.09)
Bldgid<-c(1,2,3,4,5,5,6,7,7)
DF=cbind(Acres,Bldgid)
DF<-as.data.frame(DF)
So that:
Acres Bldgid
1 100.00 1
2 101.00 2
3 100.00 3
4 130.00 4
5 156.00 5
2008 Nov 06
7
utorrent does not start
Code:
/mnt/shetach/Downloads/utorrent# wine ./ut161L.exe /RECOVER
err:module:import_dll Library (which is needed by L"W:\\Downloads\\utorrent\\ut161L.exe") not found
err:module:LdrInitializeThunk Main exe initialization for L"W:\\Downloads\\utorrent\\ut161L.exe" failed, status c0000135
I would like some help to determine what that means, I suspect a missing DLL but I
2015 Dec 16
2
samba4 schema for openldap
On 16/12/15 20:40, Таболин Юрий wrote:
> 16.12.2015 22:47, Rowland penny пишет:
>> On 16/12/15 19:35, Rowland penny wrote:
>>> On 16/12/15 19:02, Таболин Юрий wrote:
>>>> Hi all.
>>>>
>>>> I have samba 4.2.3 on freebsd 10.1 server. There are three DC and
>>>> about 350 PC on domain. I wrote earlier that samba4 ldap
2015 Dec 16
3
samba4 schema for openldap
On 16/12/15 19:35, Rowland penny wrote:
> On 16/12/15 19:02, Таболин Юрий wrote:
>> Hi all.
>>
>> I have samba 4.2.3 on freebsd 10.1 server. There are three DC and
>> about 350 PC on domain. I wrote earlier that samba4 ldap performance
>> is not enough for me. Now I want to try a server in the middle with
>> openldap pcache - ldap cache proxy function. But
2015 Dec 16
2
samba4 schema for openldap
On Wed, Dec 16, 2015 at 12:40 PM, Таболин Юрий <tabolin at speechpro.com>
wrote:
> 16.12.2015 22:47, Rowland penny пишет:
>
>> On 16/12/15 19:35, Rowland penny wrote:
>>
>>> On 16/12/15 19:02, Таболин Юрий wrote:
>>>
>>>> Hi all.
>>>>
>>>> I have samba 4.2.3 on freebsd 10.1 server. There are three DC and about
2004 Dec 17
0
Total newbie here looking to do a VoIP conferencecall?
Patrick hi.
Asterisk can do that, and you don't need VOIP lines.
If you connect Asterisk to the net, and all employees have a VOIP phone
(either hardware or software) then you're good to go.
What do you need?
To begin with, install linux on an old pc (well, not too old).
Then go to voip-info.org and take a look at the Asterisk wiki.
Everything you need is there.
And of course, we're
2015 Dec 16
0
samba4 schema for openldap
16.12.2015 22:47, Rowland penny пишет:
> On 16/12/15 19:35, Rowland penny wrote:
>> On 16/12/15 19:02, Таболин Юрий wrote:
>>> Hi all.
>>>
>>> I have samba 4.2.3 on freebsd 10.1 server. There are three DC and
>>> about 350 PC on domain. I wrote earlier that samba4 ldap performance
>>> is not enough for me. Now I want to try a server in the
2015 Dec 17
0
samba4 schema for openldap
17.12.2015 0:27, Rowland penny пишет:
> On 16/12/15 20:40, Таболин Юрий wrote:
>> 16.12.2015 22:47, Rowland penny пишет:
>>> On 16/12/15 19:35, Rowland penny wrote:
>>>> On 16/12/15 19:02, Таболин Юрий wrote:
>>>>> Hi all.
>>>>>
>>>>> I have samba 4.2.3 on freebsd 10.1 server. There are three DC and
>>>>>
2015 Dec 16
0
samba4 schema for openldap
Assuming the DNS for the site is setup correctly, the srv records should be
evenly spreading the load among the servers on the site that the client is
on.
With Windows based domain the answer to this question is either fix your
ldap client to use the SRV records and not use only the DC with the PDC
Emulator role, or add more DCs to the site. I would assume the answer is
the same for a Samba