User: Venu Pullabhatla

Reputation:
40
Status:
New User
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Last seen:
2 years ago
Joined:
6 years, 1 month ago
Email:
v***************@kcl.ac.uk

Posts by Venu Pullabhatla

<prev • 7 results • page 1 of 1 • next >
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Raw read count Vs EdgeR normzlized read count for RUVg normalization
... Hi All I am working on an RNASeq project with 2 groups of 7 samples each. The libraries contain spike-in controls (ERCC's) to be able to use for normalization. I am using RUVSeq (RUVg) package to perform this. I understand that the choice of "k" has a robust effect to calculate factors of unwanted ...
rnaseq normalization ruvseq written 2.1 years ago by Venu Pullabhatla40 • updated 2.1 years ago by davide risso780
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Very low EdgeR Pvalues with very small sample size
... Dear EdgeR users I am working on a RNASeq dataset with extremely small sample size (2 samples in each group; N=4) and I am trying to find any DEG's using these samples (I am aware of the consequences of using very small sample size). I did find some DEG's with P.values as low as 6.9e-17 and an equi ...
edger sample size pvalue written 2.5 years ago by Venu Pullabhatla40 • updated 2.5 years ago by Aaron Lun21k
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CNAnorm ploidy help
... Hi CNAnorm users I am using CNAnorm for identifying somatic CNV's from shallow WGS of FFPE samples. I have access to the tumor and the paired control samples. I have used CNAnorm on one of the pairs and managed to get the genome output. I see that the estimated ploidy for this sample is 5. I know t ...
dnacopy cnanorm written 3.0 years ago by Venu Pullabhatla40 • updated 3.0 years ago by s.berri0
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Comment: C: CRLMM Annotation file
... Hi Jim Many thanks for your prompt response. I am surprised to know about crlmm specificity to Affymetrix because the vignette claims to be applicable for Illumina platforms also. I am referring to the following vignette. http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst /doc/ ...
written 4.8 years ago by Venu Pullabhatla40
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CRLMM Annotation file
... Hi All I am working on Illumina HumanOmni5MExome-4v1-1_A SNP array to identify CNV's and LOH's from this data. I have come across "crlmm" package that can do this and started following the "Preprocessing and Genotyping Illumina Arrays for Copy Number Analysis" vignette. I realized that the crlmm pa ...
snp annotation cdf written 4.8 years ago by Venu Pullabhatla40 • updated 4.8 years ago by James W. MacDonald48k
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Answer: A: limma topTable doesn't work without replicates [was: Help with limma]
... Dear Gordon Thank you very much for your help. I got it working now and also sorry for not keeping the discussion on the list. Best wishes Venu On 15/10/12 23:02, Gordon K Smyth wrote: > Dear Venu, > > Please keep the discussion on the list. > > log2-fold-changes are contained i ...
written 6.2 years ago by Venu Pullabhatla40
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Help with Limma
... Dear Limma users After finishing the analysis successfully with replicates, I am now trying to analyze the same without replicates. After following a suggestion that I can use Limma without applying the fit2 <- eBayes(fit2) step (for without replicates), I tried to do the same for just one of th ...
limma written 6.2 years ago by Venu Pullabhatla40 • updated 6.2 years ago by James W. MacDonald48k

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