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Forum: Illumina/Solexa 10-30-2014, 12:09 AM
Replies: 0
Views: 947
Posted By xfh
Post whether the unique mapping reads should be extracted in Small RNA-Seq

Dear all,
here i have a question "whether the unique mapping reads should be extracted in Small RNA-Seq".

i have some datasets, useing bowtie for mapping the reads, only about 30% of the mapping...
Forum: Bioinformatics 02-18-2014, 05:04 PM
Replies: 4
Views: 712
Posted By xfh
thank you very much again, someone told me that...

thank you very much again, someone told me that the dataset can be fitting with R package "spline.smooth" first and then make ANCOVA ~
Forum: Bioinformatics 02-18-2014, 04:18 PM
Replies: 4
Views: 712
Posted By xfh
thank you for your information. and here i want...

thank you for your information. and here i want to ask how to handle the dataset. because the age and number of samples are different. the data is not paired. like ancova(x,y), the vector x,y should...
Forum: Bioinformatics 02-18-2014, 05:45 AM
Replies: 4
Views: 712
Posted By xfh
Post how to make ANCOVA in two indenpendent dataset

for example, there are two gene expression microarray datasets,

samples 1
gene 14 year-old 25 year-old .....

LDH 0.2 0.8 ....

samples 2
gene 12...
Forum: Bioinformatics 11-25-2013, 09:27 PM
Replies: 0
Views: 826
Posted By xfh
Post how to remove the outlier samples in gene microarray analysis

We used principal component (PC) analysis to identify and remove outlier
samples. We converted each sample into a z score statistic, based on the
squared distance of its 1st PC from the population...
Forum: Bioinformatics 10-10-2013, 06:46 PM
Replies: 12
Views: 6,095
Posted By xfh
I also have the same warning message with...

I also have the same warning message with Homo_sapiens.GRCh37.71.dna.toplevel reference. anyone can explain it?
Forum: Bioinformatics 09-22-2013, 07:45 PM
Replies: 2
Views: 1,793
Posted By xfh
I have resolved that problem, thank you very much ~~~

i install libxml2-dev and r-cran-rgl, then the dependency problem was be resolved.
Forum: Bioinformatics 09-22-2013, 07:42 PM
Replies: 0
Views: 1,447
Posted By xfh
Post about the GEO Illumina methylation 450K array data

Dear all,

I want to learn the data analysis of Illumina methylation 450K chip, I found there are several files on the GEO database, like SOFT, TXT, GSE....tar, I didn't fully understand the...
Forum: Bioinformatics 09-22-2013, 01:12 AM
Replies: 2
Views: 1,793
Posted By xfh
Post about installation of lumi, a R package used in methylation array data analysis

Dear all,
I have a problem in the installation of lumi. My R version is 3.0.1, bioconductor is 2.12, and I used the command source("http://bioconductor.org/biocLite.R"); biocLite("lumi"). however,...
Forum: Bioinformatics 09-03-2013, 05:30 PM
Replies: 8
Views: 9,192
Posted By xfh
hi, i also have that problem. here the chromosome...

hi, i also have that problem. here the chromosome name is same between index and gtf. the file name of index, fa, gtf is hg18_ref. anyone can help me?
Forum: Bioinformatics 05-29-2013, 04:58 PM
Replies: 5
Views: 1,314
Posted By xfh
thank you very much.

thank you very much.
Forum: Bioinformatics 05-29-2013, 07:10 AM
Replies: 5
Views: 1,314
Posted By xfh
thanks for your reply. however, when I search...

thanks for your reply.
however, when I search a "Azheimer disease" like term, it will get many different omim number. as the web show,...
Forum: Bioinformatics 05-28-2013, 07:08 AM
Replies: 5
Views: 1,314
Posted By xfh
how to get a gene set (human) related with a disease (such as AD, CHD ...)

Dear everyone,

here I want to get all the (human )genes related with a specific disease (such as AD ...), any databases could do it? hope some suggestions, thanks all.

xiao
Forum: Bioinformatics 05-02-2013, 05:38 PM
Replies: 4
Views: 3,360
Posted By xfh
OKay, thank you!

OKay, thank you!
Forum: Bioinformatics 04-12-2013, 11:03 PM
Replies: 4
Views: 3,360
Posted By xfh
Dear Xi, here I have a problem in installation...

Dear Xi,
here I have a problem in installation of BSMAP, my system is opensuse 12.3 x86_64 GNU/Linux. and when I make the software, the errors:
[email protected]:~/Software/bsmap-2.74> make
g++...
Forum: Bioinformatics 03-24-2013, 11:54 PM
Replies: 0
Views: 719
Posted By xfh
sequence set motifs over-represented analysis

Dear everyone,

Here I have a question. There are some DMRs (differently methylated regions), which detected by case-control analysis. The specie is Human. however, only few of them located near...
Forum: Bioinformatics 03-15-2013, 01:01 AM
Replies: 4
Views: 1,017
Posted By xfh
this tool is very good, thank you very much.

this tool is very good, thank you very much.
Forum: Bioinformatics 03-15-2013, 01:00 AM
Replies: 4
Views: 1,017
Posted By xfh
get it, thank you.

get it, thank you.
Forum: Bioinformatics 03-14-2013, 05:35 PM
Replies: 4
Views: 1,017
Posted By xfh
Post what tools could plot a picture like this

Dear everyone,

I want to know how this kind picture is plotted, could you help me? Just mark the target regions on each chromosome.

thank you.
Forum: Bioinformatics 03-12-2013, 04:32 AM
Replies: 4
Views: 1,128
Posted By xfh
nice, thank you very much.

nice, thank you very much.
Forum: Bioinformatics 03-12-2013, 12:36 AM
Replies: 4
Views: 1,128
Posted By xfh
thank you, I will have try.

thank you, I will have try.
Forum: Bioinformatics 03-12-2013, 12:26 AM
Replies: 4
Views: 1,128
Posted By xfh
how to find the relationship of dozens genes

Dear all researches,

here I have a problem and need some help. I have a gene set (deceted by case-control methylome analysis) related with type-2 diabetes. and I want to construct a network to...
Forum: Illumina/Solexa 01-15-2013, 05:26 PM
Replies: 6
Views: 1,135
Posted By xfh
Great, I will use seqdiverse to make a try, thank...

Great, I will use seqdiverse to make a try, thank you very much.
Forum: Illumina/Solexa 01-15-2013, 03:57 PM
Replies: 6
Views: 1,135
Posted By xfh
thank all for your reply, i will have a try.

thank all for your reply, i will have a try.
Forum: Illumina/Solexa 01-14-2013, 05:25 PM
Replies: 6
Views: 1,135
Posted By xfh
how could I know whether the adaptor has been trimed

Dear all,

Here I have a question about the data analysis about NGS. I download the pair-end fastq files about WGBS on EBI, but I don't know what is the adaptor that used and I want to ask how can...
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