Moderator: Asaf
Asaf ♦ 8.5k
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Posts by Asaf
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... I think that the problem is that lncRNA <-> GO/KEGG mapping is pretty poor (especially KEGG). In other words, I don't think it's a technical issue, I think it's a real issue. ...
written 12 hours ago by
Asaf ♦ 8.5k
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Comment:
C: Problem with design for DESeq2
... Patient 13 appears in A and B ...
written 13 hours ago by
Asaf ♦ 8.5k
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... The easy way to compare two gene lists is to compare list1 vs union(list1, list2) so the background should be both lists so the Fisher's exact test is ((list1 & GO), (list1 - GO), (all-list1& GO, all-list1 - GO)). Just watch out for overlap of the lists and how to interpret the results in th ...
written 3 days ago by
Asaf ♦ 8.5k
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... 1. The background is the group of all the genes in the genome. If you entered genes which are not in the genome DAVID will ignore them and they will be dropped from the list.
2. For each analysis the background might be different. If the mapping of gene <-> GO term was done on a set of genes d ...
written 3 days ago by
Asaf ♦ 8.5k
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... We Used to do it using sequencher. It is manual and laborious but we went through hundreds of chromatograms to verify the sequencing. ...
written 4 days ago by
Asaf ♦ 8.5k
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Comment:
C: from protein to tRNA combinations
... I mean that in python you should indent each clause, e.g.:
def foo(fn):
print(a)
if (fn>8):
print(fn) ...
written 26 days ago by
Asaf ♦ 8.5k
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Comment:
C: from protein to tRNA combinations
... The function is not indented, is it like this in the original script? ...
written 26 days ago by
Asaf ♦ 8.5k
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... They might be separated by PC3, who knows. Since the first PC is separating the two outliers than the rest, removing them should change the PCA and you might get a separation. Even if not, you shouldn't remove these samples. ...
written 3 months ago by
Asaf ♦ 8.5k
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... The two allergic samples on the far right look suspicious, I'm sure that removing them will result with a better-looking PCA plot, you should try to understand what makes them so different than the rest of the samples. ...
written 3 months ago by
Asaf ♦ 8.5k
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Comment:
C: Defining groups in Geo2R
... Yeah, that's weird, it only has the M9 replicates. You should probably email the corresponding author and ask them. ...
written 3 months ago by
Asaf ♦ 8.5k
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