User: mccormack

gravatar for mccormack
mccormack40
Reputation:
40
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New User
Location:
United States
Last seen:
8 months, 1 week ago
Joined:
5 years, 11 months ago
Email:
m********@molbio.mgh.harvard.edu

Posts by mccormack

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Collapse rows of dataframe by AGI transcript numbers to AGI gene number
... Great ! Does the job very well. Thank you. ...
written 8 months ago by mccormack40
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Collapse rows of dataframe by AGI transcript numbers to AGI gene number
... I have a data frame in which the first column contains unique identifiers in the form of Arabidopsis AGI transcript numbers. target_id est_counts tpm AT1G01010.1 236 26.3 AT1G01020.2 55.0 12.2 AT1G01020.6 0 0 AT1G01020.1 25.2 4.8 AT1G0 ...
R written 8 months ago by mccormack40 • updated 8 months ago by zx87549.4k
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Comment: C: How to extract bigWig signal for a given bed file?
... Great ! Thank you very much. Works very well. Numbers for all the ATGs (genes). ...
written 19 months ago by mccormack40
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Comment: C: How to extract bigWig signal for a given bed file?
... Hi Devon, Thank you very much for this script. I added three lines where you have the comment, 'Do something with the values': ATG = cols[3] # get the identifier from the bed file span = sum(vals) # sum all the values in vals print(ATG,"\t",span,"\n") This print ...
written 19 months ago by mccormack40
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Comment: C: DESeq2 results difference between use of lfcThreshold and sequential cutoffs.
... For Method A, the DESeq2 command is: res_WTK_WTN <- results(dds, contrast=c("condition", "WT-N", "WT-K")) The results of above are written into a tab-delimited .txt file and all genes with a FDR > 0.05 are removed. With the remaining genes, all genes with a log(2) of > 1 or < -1 a ...
written 2.1 years ago by mccormack40
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Comment: C: DESeq2 results difference between use of lfcThreshold and sequential cutoffs.
... I am not sure I understand. In my thinking, to take from your example in which all of the statistically significant genes (ssg), p-adj 0.05 or less, had a log(2) of between 1 and -1, then in Method A the ssg make it thru the initial FDR 0.05 cutoff while all the log(2) 1 genes are deleted in this st ...
written 2.1 years ago by mccormack40
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DESeq2 results difference between use of lfcThreshold and sequential cutoffs.
... I had been doing analysis using DESeq2 such that I would get the results from DESeq2, do a FDR (adj p-value) cutoff of 0.05 and then from that resulting list do a log(2) cutoff of greater than 1 and less than -1. I will call this Method A, 'sequential cutoffs' I have come to realize that the final ...
deseq2 written 2.1 years ago by mccormack40 • updated 2.1 years ago by cpad011213k
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RNA seq analysis when many genes are differentially expressed
... I know that many, if not all, differential expression analyses of RNA seq data assume that the majority of genes are not changing expression. However, what if you have data that when a FDR cutoff of 0.05 is used there are 30%, 40% or even 50% of genes are differentially expressed ? What distortion ...
deseq2 cuffdiff rna-seq edger written 2.4 years ago by mccormack40 • updated 2.4 years ago by Kevin Blighe61k
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Comment: C: HTSeq special counters occur at top and bottom of output file
... We could do this, but the HTSeq was fine for 16 of the 24 samples. It was only 8 samples that had this problem and I do not see any difference in the commands (other than file names) between samples that worked and samples that resulted in the special counters at the top and bottom of the output. ...
written 2.6 years ago by mccormack40
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Comment: C: HTSeq special counters occur at top and bottom of output file
... The BSUB -o command sends the output to the file named HTseq_S1_HTseq.txt. But, even if it were appending, why would it append only the special counters and not the count data ? ...
written 2.6 years ago by mccormack40

Latest awards to mccormack

Popular Question 19 months ago, created a question with more than 1,000 views. For block design with time course and DESeq2
Popular Question 19 months ago, created a question with more than 1,000 views. For -nan for FPKM value in Cuffdiff output
Popular Question 19 months ago, created a question with more than 1,000 views. For cluster groups of values disregarding specific sequence of values

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