User: dhwani.dholakia

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Posts by dhwani.dholakia

<prev • 22 results • page 1 of 3 • next >
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How to plot the batch corrected values in DESeq2
... Hello, I have used DESeq2 for differential analysis of small RNA data. I wanted to plot jitter plot of top most differentialy expressed gene using the **plotCounts** function. When i plot them i can still see the batch effect in the image generated.I then refereed to your post https://support.biocon ...
normalization deseq2 written 6 months ago by dhwani.dholakia0 • updated 6 months ago by Michael Love24k
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Answer: A: Upgrade to 3.1 error
...   Just run the below script to get latest version of R However before installing the R it is advisable to remove the installed r To run the script you have to make the script executable type the command chmod +x script name then run in terminal ./script   ### Script to update R ### ------- ...
written 4.2 years ago by dhwani.dholakia0 • updated 4.2 years ago by Martin Morgan ♦♦ 23k
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Remove coexpressed gene pair modules using eisa package
... how to remove modules in which more than a specific percentage(15%) of gene pairs exhibited high co expression with a correlation value more than .7 ...
microarray eisa affymetrix isa2 written 4.2 years ago by dhwani.dholakia0
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Biclustering approach to make transcription modules for rna seq data
... Is it possible to make transcription modules for rna seq data using biclustering approach ...
rnaseq eisa bicluster trancription modules isa written 4.2 years ago by dhwani.dholakia0
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what is the input file to isa2 package
... Input to isa package is a normalised matrix of expression file(rwa) or  matrix with fold change value  ...
eisa isa2 written 4.2 years ago by dhwani.dholakia0
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Comment: C: RMA normaliztion using XPS
... after your prevuous comments i updated xps to 1.22 version and or annotation i am using na35  ...
written 4.2 years ago by dhwani.dholakia0
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Comment: C: RMA normaliztion using XPS
... Thank you so much sir for all your information finally i am able to use xps smoothly however probes names vary when normalised using affy package ...
written 4.2 years ago by dhwani.dholakia0
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Comment: C: RMA normaliztion using XPS
... Below is the command history of my xps rma normalization. please help me to identify the error in script as the values after normalization varies in wide range 10 - 39000 celdir <- "/home/dhwani/Desktop/cmap_data/final_cmap_filtering/array_specific/ht_all/" scheme.test3 <- root.scheme("/home/ ...
written 4.3 years ago by dhwani.dholakia0
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Best way to load .cel files so as it consumes less memory
... I have 4000 .CEL files and i am unable to read it using the below command. i am in the path where .CEL files are there data <-ReadAffy() what else option can be used so that it becomes memory efficient ...
affy read in cel files written 4.3 years ago by dhwani.dholakia0 • updated 4.3 years ago by svlachavas660
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Comment: C: RMA normaliztion using XPS
... savehistory(file = ".Rhistory") this command doesnt work to save history . what is the way i can save history so that i can so u my commands if there was some error in commands ...
written 4.3 years ago by dhwani.dholakia0

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For RMA normaliztion using XPS

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