User: cankutcubuk

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cankutcubuk170
Reputation:
170
Status:
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Location:
Spain
Last seen:
3 years, 1 month ago
Joined:
4 years, 3 months ago
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c**********@gmail.com

Cankut CUBUK
Computational Genomics Program - Systems Genomics Lab
Centro de Investigación Príncipe Felipe (CIPF)
C/ Eduardo Primo Yúfera nº3
46012 Valencia, Spain
http://bioinfo.cipf.es ​
mlpm.eu

Posts by cankutcubuk

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Remove Batch Effect From RNAseq with SVAseq and Combat
... Hi Yasin, Sorry for my late reply. You are right. svaseq does it internally. I missed this part. You can skip the log transformation before using svaseq. Taken from svaseq: The function takes log(dat + constant) before performing sva. By default constant = 1, all values of dat + constant should be p ...
written 3.2 years ago by cankutcubuk170
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Lung Adenocarcinoma (TCGAProvisional) Clinical Data Unknown Sample Name
... Hi, I downloaded clinical data of lung adenocarcinoma(TCGAProvisional) from www.cbioportal.org There is a sample called "Val.Stat". Does this have any meaning? http://www.cbioportal.org/case.do?cancer_study_id=luad_tcga&sample_id=Val.Stat Cheers Cankut ...
cbioportal luad clinical data written 3.6 years ago by cankutcubuk170
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Comment: C: Phosphorylation capacity of an enzyme
... Hi Daniel, Thank you for your correction and advise. Best Wishes Cankut ...
written 3.8 years ago by cankutcubuk170
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(Closed) Phosphorylation capacity of an enzyme
... Dear All, My question is more biochemistry related. However, I need this information to perform a bioinformatic analysis. Let's think ProteinA can phosphorylate proteinB, proteinC and proteinD. Condition1: All proteins are expressed and proteinA phosphorylates proteinB, proteinC and proteinD.  C ...
metabolic reaction protein phosphorylation enzyme written 3.8 years ago by cankutcubuk170
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Comment: C: Remove Batch Effect From RNAseq with SVAseq and Combat
... Hi Raunakms, thanks for your reply. Cheers ...
written 3.8 years ago by cankutcubuk170
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Remove Batch Effect From RNAseq with SVAseq and Combat
... Hi, I need your help and comments to remove batch effect from RNA-Seq data.  In total I have almost 1000 RNA-Seq data of different cancer types. Each cancer type has control and tumor groups. There is 1 batch covariate. The idea is to remove the batch effect from all data at once. First question: ...
combat svaseq model.matrix rna-seq batch effect written 4.2 years ago by cankutcubuk170 • updated 2.8 years ago by amoltej90
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Comment: C: Strange Gene Ids In Tcga
... Ok I will do, thanks ...
written 4.3 years ago by cankutcubuk170
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Answer: A: Strange Gene Ids In Tcga
... I have an other question. Some of the gene_IDs has string extension as "_calculated" What does it mean? Example: ==> OV__bcgsc.ca__illuminahiseq_rnaseq__gene.quantification__Jul-08-2014.txt <== Hybridization REF gene ?|100132510_calculated ?|100134860_calculated ?|10357_calculated ?|10431 ...
written 4.3 years ago by cankutcubuk170
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Answer: A: To What Degree Could We Determine Whether A Gene Is Expressed?
... Hi, Can I apply the zFPKM approach by RPKM data(zRPKM)? Or which kind of normalization methods are compatible with this method? By the way, here you can find the R script for zFPKM normalization. I inspired from the python code which has given above. install.packages("ks","pracma") library(k ...
written 4.3 years ago by cankutcubuk170

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For Remove Batch Effect From RNAseq with SVAseq and Combat
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