User: vinayjrao
vinayjrao • 170
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Posts by vinayjrao
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... Hi,
I am working on some whole exome data, which were annotated using the web based ANNOVAR (wANNOVAR). I downloaded the `.csv` output. When I open the file with Excel, a) my laptop slows down quite a lot, and b) there are a lot of columns, which lead to making errors at times. Below is a sample of ...
written 2 days ago by
vinayjrao • 170
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50
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... Hi,
I am analyzing whole exome data to analyze InDels and SNPs between healthy control and diseased patients. Since I'm new to analyzing exome data, I would like to know whether I should remove all duplicates or only sequencing duplicates, because removing all duplicates can also result in neglecti ...
written 3 days ago by
vinayjrao • 170
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... Thank you both for the insight. Although, it is still not clear to me whether a decrease in fastq file size will linearly reduce the number of variants? ...
written 4 months ago by
vinayjrao • 170
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... Hi,
I analyzed a few human Exome-Seq data sets, and I noticed that their fastq files were around 2.5 Gb each. I am analyzing another set, where the fastq files are around 900 Mb. After aligning both with hg38, and following the same pipeline, I noticed upon variant calling (GATK HaplotypeCaller) th ...
3
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... Hi,
I am working with a microarray dataset, which is in the format -
> Control Control2 Treatment Treatment2
The dataset has been log transformed. I want to know if there a way to filter the data such that I get genes whose fold difference is greater than 2 fold in Treatment as ...
written 12 months ago by
vinayjrao • 170
• updated
12 months ago by
Nicolas Rosewick ♦ 8.8k
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Comment:
C: Averaging multiple columns
... Thank you for your help. It works perfectly. ...
written 12 months ago by
vinayjrao • 170
0
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2
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317
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2
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Comment:
C: Averaging multiple columns
... Thank you for your reply. I am still working on it.
Will update once done. ...
written 12 months ago by
vinayjrao • 170
4
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2
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317
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2
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... Hi,
I have a file with five columns, from which I want the mean of the last four columns where the first rows of the first column are the same. For example, my file looks like this -
A 1 1 1 1
A 1 3 1 1
A 1 1 2 3
B 5 7 2 4
C 2 1 5 1
C 2 2 3 6
The desired output is -
A ...
1
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1
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1.4k
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1
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... Hi,
I have two data frames, both containing the columns `GeneName` and `logFC`.
Using `intersect()`, I have obtained the common genes between the two. I want to know how to merge my two dataframes based on the common dataframe.
Thank you. ...
written 12 months ago by
vinayjrao • 170
• updated
12 months ago by
lakhujanivijay ♦ 5.0k
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305
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... Thanks Kevin, for the clarification. Although, I would like to know why I should remove these after normalization, and what is the significance of these positive control probes? ...
written 12 months ago by
vinayjrao • 170
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