Moderator: Santosh Anand

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Santosh Anand4.8k
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Posts by Santosh Anand

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Comment: C: Design Formula With DESeq2
... since you are interested in the effect of the combination of CELLTYPE and COMPCHLES, you may create a new grouping as follows newGroup = paste0(CELLTYPE, "_", COMPCHLES) Then use only `newGroup` in your design formula. It's level will contain all the combinations of CELLTYPE & COMPCHLES. ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: Design Formula With DESeq2
... yes, that's the right interpretation ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... Upvoted. You may accept your own answer to close this thread ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... To solve this, you can always use the complete path of the correct JAVA (inside R or outside also), something like `/usr/local/bin/java`. To know the correct path, write `which java` on commandline. ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: Design Formula With DESeq2
... BTW, this thread will definitely help you if you are new to the design formula: https://www.biostars.org/p/278684/ Esp., check this reply from Michael Love (Developer of DESeq2) https://www.biostars.org/p/278684/#354121 ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: Annotating entrez Ids with the kegg pathway they are involved in
... did you do any search by yourself? what did you get? ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: Design Formula With DESeq2
... The rank of a model matrix, loosely speaking, is the maximum number of linearly independent columns to define the model. The info in your STATUS column is contained in the COMPCHLES column, as also told by swbarnes2 in the answer section. That is why, the model.matrix is not full rank and you need ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... What was your problem with JAVA. BTW, why use R to run a shell-script (BQSR)? ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... Did you encounter any error? Could you just run BQSR on a single sample using commandline directly (wihout R)? ...
written 5 days ago by Santosh Anand4.8k
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Comment: C: FastQC before and after Base Quality Score Recalibration (BQSR)
... That is extremely weird. How did you run BQSR? ...
written 6 days ago by Santosh Anand4.8k

Latest awards to Santosh Anand

Great Question 1 day ago, created a question with more than 5,000 views. For chart title in plotly (R)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For chart title in plotly (R)
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: How to import huge .csv files in R studio?
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: How to import huge .csv files in R studio?
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 4 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Scholar 5 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Scholar 7 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Popular Question 7 months ago, created a question with more than 1,000 views. For chart title in plotly (R)
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to import huge .csv files in R studio?
Scholar 10 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: How to import huge .csv files in R studio?
Popular Question 10 months ago, created a question with more than 1,000 views. For chart title in plotly (R)

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